... | ... |
@@ -1,6 +1,9 @@ |
1 |
+# celda v1.9.3 (2021-10-04) |
|
2 |
+ |
|
1 | 3 |
* Fixed bug in checking background matrix with decontX |
2 | 4 |
* Switched to using Github Actions for Continuous Integration |
3 | 5 |
* Fixed plotting bugs in celda results reports |
6 |
+* Speed up final step in decontX when creating final decontaminated matrix |
|
4 | 7 |
|
5 | 8 |
# celda v1.9.2 (2021-07-19) |
6 | 9 |
|
... | ... |
@@ -34,6 +34,7 @@ reference: |
34 | 34 |
- plotDecontXContamination |
35 | 35 |
- plotDecontXMarkerExpression |
36 | 36 |
- plotDecontXMarkerPercentage |
37 |
+ |
|
37 | 38 |
- decontXcounts |
38 | 39 |
|
39 | 40 |
- title: Functions for determining the numbers of clusters in celda |
... | ... |
@@ -101,7 +102,7 @@ navbar: |
101 | 102 |
title: "celda" |
102 | 103 |
left: |
103 | 104 |
- icon: fa-home fa-lg |
104 |
- href: http://celda.camplab.net/ |
|
105 |
+ href: https://www.camplab.net/celda |
|
105 | 106 |
- text: "Installation" |
106 | 107 |
href: articles/articles/installation.html |
107 | 108 |
- text: "Vignettes" |
... | ... |
@@ -71,14 +71,14 @@ |
71 | 71 |
</button> |
72 | 72 |
<span class="navbar-brand"> |
73 | 73 |
<a class="navbar-link" href="index.html">celda</a> |
74 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
74 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
75 | 75 |
</span> |
76 | 76 |
</div> |
77 | 77 |
|
78 | 78 |
<div id="navbar" class="navbar-collapse collapse"> |
79 | 79 |
<ul class="nav navbar-nav"> |
80 | 80 |
<li> |
81 |
- <a href="http://celda.camplab.net/"> |
|
81 |
+ <a href="https://www.camplab.net/celda"> |
|
82 | 82 |
<span class="fas fa-home fa-lg"></span> |
83 | 83 |
|
84 | 84 |
</a> |
... | ... |
@@ -71,14 +71,14 @@ |
71 | 71 |
</button> |
72 | 72 |
<span class="navbar-brand"> |
73 | 73 |
<a class="navbar-link" href="index.html">celda</a> |
74 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
74 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
75 | 75 |
</span> |
76 | 76 |
</div> |
77 | 77 |
|
78 | 78 |
<div id="navbar" class="navbar-collapse collapse"> |
79 | 79 |
<ul class="nav navbar-nav"> |
80 | 80 |
<li> |
81 |
- <a href="http://celda.camplab.net/"> |
|
81 |
+ <a href="https://www.camplab.net/celda"> |
|
82 | 82 |
<span class="fas fa-home fa-lg"></span> |
83 | 83 |
|
84 | 84 |
</a> |
... | ... |
@@ -71,14 +71,14 @@ |
71 | 71 |
</button> |
72 | 72 |
<span class="navbar-brand"> |
73 | 73 |
<a class="navbar-link" href="index.html">celda</a> |
74 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
74 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
75 | 75 |
</span> |
76 | 76 |
</div> |
77 | 77 |
|
78 | 78 |
<div id="navbar" class="navbar-collapse collapse"> |
79 | 79 |
<ul class="nav navbar-nav"> |
80 | 80 |
<li> |
81 |
- <a href="http://celda.camplab.net/"> |
|
81 |
+ <a href="https://www.camplab.net/celda"> |
|
82 | 82 |
<span class="fas fa-home fa-lg"></span> |
83 | 83 |
|
84 | 84 |
</a> |
... | ... |
@@ -31,14 +31,14 @@ |
31 | 31 |
</button> |
32 | 32 |
<span class="navbar-brand"> |
33 | 33 |
<a class="navbar-link" href="../../index.html">celda</a> |
34 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
34 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
35 | 35 |
</span> |
36 | 36 |
</div> |
37 | 37 |
|
38 | 38 |
<div id="navbar" class="navbar-collapse collapse"> |
39 | 39 |
<ul class="nav navbar-nav"> |
40 | 40 |
<li> |
41 |
- <a href="http://celda.camplab.net/"> |
|
41 |
+ <a href="https://www.camplab.net/celda"> |
|
42 | 42 |
<span class="fas fa-home fa-lg"></span> |
43 | 43 |
|
44 | 44 |
</a> |
... | ... |
@@ -98,7 +98,7 @@ |
98 | 98 |
<h1 data-toc-skip>Celda - Analysis of PBMC3K</h1> |
99 | 99 |
<h4 class="author">Joshua Campbell, Zhe Wang</h4> |
100 | 100 |
|
101 |
- <h4 class="date">Compiled September 29, 2021</h4> |
|
101 |
+ <h4 class="date">Compiled October 04, 2021</h4> |
|
102 | 102 |
|
103 | 103 |
<small class="dont-index">Source: <a href="https://github.com/campbio/celda/blob/master/vignettes/articles/celda_pbmc3k.Rmd"><code>vignettes/articles/celda_pbmc3k.Rmd</code></a></small> |
104 | 104 |
<div class="hidden name"><code>celda_pbmc3k.Rmd</code></div> |
... | ... |
@@ -28341,7 +28341,7 @@ sessionInfo() |
28341 | 28341 |
## other attached packages: |
28342 | 28342 |
## [1] scater_1.18.6 kableExtra_1.3.4 |
28343 | 28343 |
## [3] knitr_1.31 ggplot2_3.3.5 |
28344 |
-## [5] celda_1.9.2 singleCellTK_2.2.0 |
|
28344 |
+## [5] celda_1.9.3 singleCellTK_2.2.0 |
|
28345 | 28345 |
## [7] TENxPBMCData_1.8.0 HDF5Array_1.18.1 |
28346 | 28346 |
## [9] rhdf5_2.34.0 DelayedArray_0.16.2 |
28347 | 28347 |
## [11] Matrix_1.3-2 SingleCellExperiment_1.12.0 |
... | ... |
@@ -31,14 +31,14 @@ |
31 | 31 |
</button> |
32 | 32 |
<span class="navbar-brand"> |
33 | 33 |
<a class="navbar-link" href="../../index.html">celda</a> |
34 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
34 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
35 | 35 |
</span> |
36 | 36 |
</div> |
37 | 37 |
|
38 | 38 |
<div id="navbar" class="navbar-collapse collapse"> |
39 | 39 |
<ul class="nav navbar-nav"> |
40 | 40 |
<li> |
41 |
- <a href="http://celda.camplab.net/"> |
|
41 |
+ <a href="https://www.camplab.net/celda"> |
|
42 | 42 |
<span class="fas fa-home fa-lg"></span> |
43 | 43 |
|
44 | 44 |
</a> |
... | ... |
@@ -97,7 +97,7 @@ |
97 | 97 |
<h1 data-toc-skip>DecontX - Decontamination of PBMC4K</h1> |
98 | 98 |
<h4 class="author">Joshua Campbell, Shiyi Yang, Zhe Wang, Yuan Yin</h4> |
99 | 99 |
|
100 |
- <h4 class="date">Compiled September 29, 2021</h4> |
|
100 |
+ <h4 class="date">Compiled October 04, 2021</h4> |
|
101 | 101 |
|
102 | 102 |
<small class="dont-index">Source: <a href="https://github.com/campbio/celda/blob/master/vignettes/articles/decontX_pbmc4k.Rmd"><code>vignettes/articles/decontX_pbmc4k.Rmd</code></a></small> |
103 | 103 |
<div class="hidden name"><code>decontX_pbmc4k.Rmd</code></div> |
... | ... |
@@ -305,7 +305,7 @@ |
305 | 305 |
## [11] GenomicRanges_1.42.0 GenomeInfoDb_1.26.4 |
306 | 306 |
## [13] IRanges_2.24.1 S4Vectors_0.28.1 |
307 | 307 |
## [15] BiocGenerics_0.36.0 MatrixGenerics_1.2.1 |
308 |
-## [17] matrixStats_0.58.0 celda_1.9.2 |
|
308 |
+## [17] matrixStats_0.58.0 celda_1.9.3 |
|
309 | 309 |
## |
310 | 310 |
## loaded via a namespace (and not attached): |
311 | 311 |
## [1] AnnotationHub_2.22.0 BiocFileCache_1.14.0 |
... | ... |
@@ -31,14 +31,14 @@ |
31 | 31 |
</button> |
32 | 32 |
<span class="navbar-brand"> |
33 | 33 |
<a class="navbar-link" href="../../index.html">celda</a> |
34 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
34 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
35 | 35 |
</span> |
36 | 36 |
</div> |
37 | 37 |
|
38 | 38 |
<div id="navbar" class="navbar-collapse collapse"> |
39 | 39 |
<ul class="nav navbar-nav"> |
40 | 40 |
<li> |
41 |
- <a href="http://celda.camplab.net/"> |
|
41 |
+ <a href="https://www.camplab.net/celda"> |
|
42 | 42 |
<span class="fas fa-home fa-lg"></span> |
43 | 43 |
|
44 | 44 |
</a> |
... | ... |
@@ -31,14 +31,14 @@ |
31 | 31 |
</button> |
32 | 32 |
<span class="navbar-brand"> |
33 | 33 |
<a class="navbar-link" href="../index.html">celda</a> |
34 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
34 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
35 | 35 |
</span> |
36 | 36 |
</div> |
37 | 37 |
|
38 | 38 |
<div id="navbar" class="navbar-collapse collapse"> |
39 | 39 |
<ul class="nav navbar-nav"> |
40 | 40 |
<li> |
41 |
- <a href="http://celda.camplab.net/"> |
|
41 |
+ <a href="https://www.camplab.net/celda"> |
|
42 | 42 |
<span class="fas fa-home fa-lg"></span> |
43 | 43 |
|
44 | 44 |
</a> |
... | ... |
@@ -107,7 +107,7 @@ |
107 | 107 |
<address class="author_afil"> |
108 | 108 |
Boston University School of Medicine<br><h4 class="author">Yusuke Koga</h4> |
109 | 109 |
<address class="author_afil"> |
110 |
- Boston University School of Medicine<br><h4 class="date">2021-09-29</h4> |
|
110 |
+ Boston University School of Medicine<br><h4 class="date">2021-10-04</h4> |
|
111 | 111 |
|
112 | 112 |
<small class="dont-index">Source: <a href="https://github.com/campbio/celda/blob/master/vignettes/celda.Rmd"><code>vignettes/celda.Rmd</code></a></small> |
113 | 113 |
<div class="hidden name"><code>celda.Rmd</code></div> |
... | ... |
@@ -394,7 +394,7 @@ |
394 | 394 |
## [5] GenomeInfoDb_1.26.4 IRanges_2.24.1 |
395 | 395 |
## [7] S4Vectors_0.28.1 BiocGenerics_0.36.0 |
396 | 396 |
## [9] MatrixGenerics_1.2.1 matrixStats_0.58.0 |
397 |
-## [11] celda_1.9.2 BiocStyle_2.18.1 |
|
397 |
+## [11] celda_1.9.3 BiocStyle_2.18.1 |
|
398 | 398 |
## |
399 | 399 |
## loaded via a namespace (and not attached): |
400 | 400 |
## [1] bitops_1.0-6 fs_1.5.0 |
... | ... |
@@ -31,14 +31,14 @@ |
31 | 31 |
</button> |
32 | 32 |
<span class="navbar-brand"> |
33 | 33 |
<a class="navbar-link" href="../index.html">celda</a> |
34 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
34 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
35 | 35 |
</span> |
36 | 36 |
</div> |
37 | 37 |
|
38 | 38 |
<div id="navbar" class="navbar-collapse collapse"> |
39 | 39 |
<ul class="nav navbar-nav"> |
40 | 40 |
<li> |
41 |
- <a href="http://celda.camplab.net/"> |
|
41 |
+ <a href="https://www.camplab.net/celda"> |
|
42 | 42 |
<span class="fas fa-home fa-lg"></span> |
43 | 43 |
|
44 | 44 |
</a> |
... | ... |
@@ -106,7 +106,7 @@ |
106 | 106 |
Boston University School of Medicine<br><a class="author_email" href="mailto:#"></a><a href="mailto:camp@bu.edu" class="email">camp@bu.edu</a> |
107 | 107 |
</address> |
108 | 108 |
|
109 |
- <h4 class="date">2021-09-29</h4> |
|
109 |
+ <h4 class="date">2021-10-04</h4> |
|
110 | 110 |
|
111 | 111 |
<small class="dont-index">Source: <a href="https://github.com/campbio/celda/blob/master/vignettes/decontX.Rmd"><code>vignettes/decontX.Rmd</code></a></small> |
112 | 112 |
<div class="hidden name"><code>decontX.Rmd</code></div> |
... | ... |
@@ -317,7 +317,7 @@ |
317 | 317 |
## [11] GenomicRanges_1.42.0 GenomeInfoDb_1.26.4 |
318 | 318 |
## [13] IRanges_2.24.1 S4Vectors_0.28.1 |
319 | 319 |
## [15] BiocGenerics_0.36.0 MatrixGenerics_1.2.1 |
320 |
-## [17] matrixStats_0.58.0 celda_1.9.2 |
|
320 |
+## [17] matrixStats_0.58.0 celda_1.9.3 |
|
321 | 321 |
## [19] BiocStyle_2.18.1 |
322 | 322 |
## |
323 | 323 |
## loaded via a namespace (and not attached): |
... | ... |
@@ -71,14 +71,14 @@ |
71 | 71 |
</button> |
72 | 72 |
<span class="navbar-brand"> |
73 | 73 |
<a class="navbar-link" href="../index.html">celda</a> |
74 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
74 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
75 | 75 |
</span> |
76 | 76 |
</div> |
77 | 77 |
|
78 | 78 |
<div id="navbar" class="navbar-collapse collapse"> |
79 | 79 |
<ul class="nav navbar-nav"> |
80 | 80 |
<li> |
81 |
- <a href="http://celda.camplab.net/"> |
|
81 |
+ <a href="https://www.camplab.net/celda"> |
|
82 | 82 |
<span class="fas fa-home fa-lg"></span> |
83 | 83 |
|
84 | 84 |
</a> |
... | ... |
@@ -71,14 +71,14 @@ |
71 | 71 |
</button> |
72 | 72 |
<span class="navbar-brand"> |
73 | 73 |
<a class="navbar-link" href="index.html">celda</a> |
74 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
74 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
75 | 75 |
</span> |
76 | 76 |
</div> |
77 | 77 |
|
78 | 78 |
<div id="navbar" class="navbar-collapse collapse"> |
79 | 79 |
<ul class="nav navbar-nav"> |
80 | 80 |
<li> |
81 |
- <a href="http://celda.camplab.net/"> |
|
81 |
+ <a href="https://www.camplab.net/celda"> |
|
82 | 82 |
<span class="fas fa-home fa-lg"></span> |
83 | 83 |
|
84 | 84 |
</a> |
... | ... |
@@ -37,14 +37,14 @@ |
37 | 37 |
</button> |
38 | 38 |
<span class="navbar-brand"> |
39 | 39 |
<a class="navbar-link" href="index.html">celda</a> |
40 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
40 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
41 | 41 |
</span> |
42 | 42 |
</div> |
43 | 43 |
|
44 | 44 |
<div id="navbar" class="navbar-collapse collapse"> |
45 | 45 |
<ul class="nav navbar-nav"> |
46 | 46 |
<li> |
47 |
- <a href="http://celda.camplab.net/"> |
|
47 |
+ <a href="https://www.camplab.net/celda"> |
|
48 | 48 |
<span class="fas fa-home fa-lg"></span> |
49 | 49 |
|
50 | 50 |
</a> |
... | ... |
@@ -71,14 +71,14 @@ |
71 | 71 |
</button> |
72 | 72 |
<span class="navbar-brand"> |
73 | 73 |
<a class="navbar-link" href="../index.html">celda</a> |
74 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
74 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
75 | 75 |
</span> |
76 | 76 |
</div> |
77 | 77 |
|
78 | 78 |
<div id="navbar" class="navbar-collapse collapse"> |
79 | 79 |
<ul class="nav navbar-nav"> |
80 | 80 |
<li> |
81 |
- <a href="http://celda.camplab.net/"> |
|
81 |
+ <a href="https://www.camplab.net/celda"> |
|
82 | 82 |
<span class="fas fa-home fa-lg"></span> |
83 | 83 |
|
84 | 84 |
</a> |
... | ... |
@@ -138,9 +138,19 @@ |
138 | 138 |
<small>Source: <a href='https://github.com/campbio/celda/blob/master/NEWS.md'><code>NEWS.md</code></a></small> |
139 | 139 |
</div> |
140 | 140 |
|
141 |
- <div id="celda-192" class="section level1"> |
|
141 |
+ <div id="celda-v193-2021-10-04" class="section level1"> |
|
142 |
+<h1 class="page-header" data-toc-text="1.9.3"> |
|
143 |
+<a href="#celda-v193-2021-10-04" class="anchor"></a>celda v1.9.3 (2021-10-04)</h1> |
|
144 |
+<ul> |
|
145 |
+<li>Fixed bug in checking background matrix with decontX</li> |
|
146 |
+<li>Switched to using Github Actions for Continuous Integration</li> |
|
147 |
+<li>Fixed plotting bugs in celda results reports</li> |
|
148 |
+<li>Speed up final step in decontX when creating final decontaminated matrix</li> |
|
149 |
+</ul> |
|
150 |
+</div> |
|
151 |
+ <div id="celda-v192-2021-07-19" class="section level1"> |
|
142 | 152 |
<h1 class="page-header" data-toc-text="1.9.2"> |
143 |
-<a href="#celda-192" class="anchor"></a>celda 1.9.2</h1> |
|
153 |
+<a href="#celda-v192-2021-07-19" class="anchor"></a>celda v1.9.2 (2021-07-19)</h1> |
|
144 | 154 |
<ul> |
145 | 155 |
<li>Added a <code>NEWS.md</code> file to track changes to the package.</li> |
146 | 156 |
<li>Added new tutorials and documentation generated with pkgdown.</li> |
... | ... |
@@ -149,6 +159,98 @@ |
149 | 159 |
<li>Minor bug fix when the input matrix was sparse and contained non-integer values.</li> |
150 | 160 |
<li>Several improvements to plotting functions.</li> |
151 | 161 |
</ul> |
162 |
+</div> |
|
163 |
+ <div id="celda-v177-2021-04-12" class="section level1"> |
|
164 |
+<h1 class="page-header" data-toc-text="1.7.7"> |
|
165 |
+<a href="#celda-v177-2021-04-12" class="anchor"></a>celda v1.7.7 (2021-04-12):</h1> |
|
166 |
+<ul> |
|
167 |
+<li>Added handling for sparse matrices</li> |
|
168 |
+</ul> |
|
169 |
+</div> |
|
170 |
+ <div id="celda-v176-2021-04-04" class="section level1"> |
|
171 |
+<h1 class="page-header" data-toc-text="1.7.6"> |
|
172 |
+<a href="#celda-v176-2021-04-04" class="anchor"></a>celda v1.7.6 (2021-04-04):</h1> |
|
173 |
+<ul> |
|
174 |
+<li>Added functions for creating HTML reports</li> |
|
175 |
+<li>Fixed bug in decontX plotting</li> |
|
176 |
+</ul> |
|
177 |
+</div> |
|
178 |
+ <div id="celda-v174-2021-03-09" class="section level1"> |
|
179 |
+<h1 class="page-header" data-toc-text="1.7.4"> |
|
180 |
+<a href="#celda-v174-2021-03-09" class="anchor"></a>celda v1.7.4 (2021-03-09):</h1> |
|
181 |
+<ul> |
|
182 |
+<li>Enable input of raw/droplet matrix into decontX to estimate ambient RNA</li> |
|
183 |
+</ul> |
|
184 |
+</div> |
|
185 |
+ <div id="celda-v116-2019-07-16" class="section level1"> |
|
186 |
+<h1 class="page-header" data-toc-text="1.1.6"> |
|
187 |
+<a href="#celda-v116-2019-07-16" class="anchor"></a>celda v1.1.6 (2019-07-16):</h1> |
|
188 |
+<ul> |
|
189 |
+<li>Add multiclass decision tree</li> |
|
190 |
+</ul> |
|
191 |
+</div> |
|
192 |
+ <div id="celda-v114-2019-05-28" class="section level1"> |
|
193 |
+<h1 class="page-header" data-toc-text="1.1.4"> |
|
194 |
+<a href="#celda-v114-2019-05-28" class="anchor"></a>celda v1.1.4 (2019-05-28):</h1> |
|
195 |
+<ul> |
|
196 |
+<li>Add Alternate headings support for plotDimReduceFeature</li> |
|
197 |
+</ul> |
|
198 |
+</div> |
|
199 |
+ <div id="celda-v113-2019-05-14" class="section level1"> |
|
200 |
+<h1 class="page-header" data-toc-text="1.1.3"> |
|
201 |
+<a href="#celda-v113-2019-05-14" class="anchor"></a>celda v1.1.3 (2019-05-14):</h1> |
|
202 |
+<ul> |
|
203 |
+<li>Add multiclass decision tree (MCDT) cell cluster annotation</li> |
|
204 |
+</ul> |
|
205 |
+</div> |
|
206 |
+ <div id="celda-v112-2019-05-14" class="section level1"> |
|
207 |
+<h1 class="page-header" data-toc-text="1.1.2"> |
|
208 |
+<a href="#celda-v112-2019-05-14" class="anchor"></a>celda v1.1.2 (2019-05-14):</h1> |
|
209 |
+<ul> |
|
210 |
+<li>Fix a bug in celdaHeatmap</li> |
|
211 |
+</ul> |
|
212 |
+</div> |
|
213 |
+ <div id="celda-v101-2019-05-09" class="section level1"> |
|
214 |
+<h1 class="page-header" data-toc-text="1.0.1"> |
|
215 |
+<a href="#celda-v101-2019-05-09" class="anchor"></a>celda v1.0.1 (2019-05-09):</h1> |
|
216 |
+<ul> |
|
217 |
+<li>Default seed setting to maintain reproducibility</li> |
|
218 |
+</ul> |
|
219 |
+</div> |
|
220 |
+ <div id="celda-v09934-2019-04-23" class="section level1"> |
|
221 |
+<h1 class="page-header" data-toc-text="0.99.34"> |
|
222 |
+<a href="#celda-v09934-2019-04-23" class="anchor"></a>celda v0.99.34 (2019-04-23):</h1> |
|
223 |
+<ul> |
|
224 |
+<li>Minor changes to the vignettes</li> |
|
225 |
+</ul> |
|
226 |
+</div> |
|
227 |
+ <div id="celda-v09923-2019-04-10" class="section level1"> |
|
228 |
+<h1 class="page-header" data-toc-text="0.99.23"> |
|
229 |
+<a href="#celda-v09923-2019-04-10" class="anchor"></a>celda v0.99.23 (2019-04-10):</h1> |
|
230 |
+<ul> |
|
231 |
+<li>Remove pheatmap import</li> |
|
232 |
+</ul> |
|
233 |
+</div> |
|
234 |
+ <div id="celda-v09922-2019-04-09" class="section level1"> |
|
235 |
+<h1 class="page-header" data-toc-text="0.99.22"> |
|
236 |
+<a href="#celda-v09922-2019-04-09" class="anchor"></a>celda v0.99.22 (2019-04-09):</h1> |
|
237 |
+<ul> |
|
238 |
+<li>Package celda, for bi-clustering of single-cell ’omics data.</li> |
|
239 |
+</ul> |
|
240 |
+</div> |
|
241 |
+ <div id="celda-v0998-2019-03-11" class="section level1"> |
|
242 |
+<h1 class="page-header" data-toc-text="0.99.8"> |
|
243 |
+<a href="#celda-v0998-2019-03-11" class="anchor"></a>celda v0.99.8 (2019-03-11):</h1> |
|
244 |
+<ul> |
|
245 |
+<li>Second submission to Bioconductor</li> |
|
246 |
+</ul> |
|
247 |
+</div> |
|
248 |
+ <div id="celda-v0990-2018-05-15" class="section level1"> |
|
249 |
+<h1 class="page-header" data-toc-text="0.99.0"> |
|
250 |
+<a href="#celda-v0990-2018-05-15" class="anchor"></a>celda v0.99.0 (2018-05-15):</h1> |
|
251 |
+<ul> |
|
252 |
+<li>First submission to Bioconductor</li> |
|
253 |
+</ul> |
|
152 | 254 |
</div> |
153 | 255 |
</div> |
154 | 256 |
|
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -77,14 +77,14 @@ |
77 | 77 |
</button> |
78 | 78 |
<span class="navbar-brand"> |
79 | 79 |
<a class="navbar-link" href="../index.html">celda</a> |
80 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
80 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
81 | 81 |
</span> |
82 | 82 |
</div> |
83 | 83 |
|
84 | 84 |
<div id="navbar" class="navbar-collapse collapse"> |
85 | 85 |
<ul class="nav navbar-nav"> |
86 | 86 |
<li> |
87 |
- <a href="http://celda.camplab.net/"> |
|
87 |
+ <a href="https://www.camplab.net/celda"> |
|
88 | 88 |
<span class="fas fa-home fa-lg"></span> |
89 | 89 |
|
90 | 90 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -79,14 +79,14 @@ |
79 | 79 |
</button> |
80 | 80 |
<span class="navbar-brand"> |
81 | 81 |
<a class="navbar-link" href="../index.html">celda</a> |
82 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
82 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
83 | 83 |
</span> |
84 | 84 |
</div> |
85 | 85 |
|
86 | 86 |
<div id="navbar" class="navbar-collapse collapse"> |
87 | 87 |
<ul class="nav navbar-nav"> |
88 | 88 |
<li> |
89 |
- <a href="http://celda.camplab.net/"> |
|
89 |
+ <a href="https://www.camplab.net/celda"> |
|
90 | 90 |
<span class="fas fa-home fa-lg"></span> |
91 | 91 |
|
92 | 92 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -75,14 +75,14 @@ |
75 | 75 |
</button> |
76 | 76 |
<span class="navbar-brand"> |
77 | 77 |
<a class="navbar-link" href="../index.html">celda</a> |
78 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
78 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
79 | 79 |
</span> |
80 | 80 |
</div> |
81 | 81 |
|
82 | 82 |
<div id="navbar" class="navbar-collapse collapse"> |
83 | 83 |
<ul class="nav navbar-nav"> |
84 | 84 |
<li> |
85 |
- <a href="http://celda.camplab.net/"> |
|
85 |
+ <a href="https://www.camplab.net/celda"> |
|
86 | 86 |
<span class="fas fa-home fa-lg"></span> |
87 | 87 |
|
88 | 88 |
</a> |
... | ... |
@@ -75,14 +75,14 @@ |
75 | 75 |
</button> |
76 | 76 |
<span class="navbar-brand"> |
77 | 77 |
<a class="navbar-link" href="../index.html">celda</a> |
78 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
78 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
79 | 79 |
</span> |
80 | 80 |
</div> |
81 | 81 |
|
82 | 82 |
<div id="navbar" class="navbar-collapse collapse"> |
83 | 83 |
<ul class="nav navbar-nav"> |
84 | 84 |
<li> |
85 |
- <a href="http://celda.camplab.net/"> |
|
85 |
+ <a href="https://www.camplab.net/celda"> |
|
86 | 86 |
<span class="fas fa-home fa-lg"></span> |
87 | 87 |
|
88 | 88 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -74,14 +74,14 @@ |
74 | 74 |
</button> |
75 | 75 |
<span class="navbar-brand"> |
76 | 76 |
<a class="navbar-link" href="../index.html">celda</a> |
77 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
77 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
78 | 78 |
</span> |
79 | 79 |
</div> |
80 | 80 |
|
81 | 81 |
<div id="navbar" class="navbar-collapse collapse"> |
82 | 82 |
<ul class="nav navbar-nav"> |
83 | 83 |
<li> |
84 |
- <a href="http://celda.camplab.net/"> |
|
84 |
+ <a href="https://www.camplab.net/celda"> |
|
85 | 85 |
<span class="fas fa-home fa-lg"></span> |
86 | 86 |
|
87 | 87 |
</a> |
... | ... |
@@ -79,14 +79,14 @@ |
79 | 79 |
</button> |
80 | 80 |
<span class="navbar-brand"> |
81 | 81 |
<a class="navbar-link" href="../index.html">celda</a> |
82 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
82 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
83 | 83 |
</span> |
84 | 84 |
</div> |
85 | 85 |
|
86 | 86 |
<div id="navbar" class="navbar-collapse collapse"> |
87 | 87 |
<ul class="nav navbar-nav"> |
88 | 88 |
<li> |
89 |
- <a href="http://celda.camplab.net/"> |
|
89 |
+ <a href="https://www.camplab.net/celda"> |
|
90 | 90 |
<span class="fas fa-home fa-lg"></span> |
91 | 91 |
|
92 | 92 |
</a> |
... | ... |
@@ -79,14 +79,14 @@ |
79 | 79 |
</button> |
80 | 80 |
<span class="navbar-brand"> |
81 | 81 |
<a class="navbar-link" href="../index.html">celda</a> |
82 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
82 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
83 | 83 |
</span> |
84 | 84 |
</div> |
85 | 85 |
|
86 | 86 |
<div id="navbar" class="navbar-collapse collapse"> |
87 | 87 |
<ul class="nav navbar-nav"> |
88 | 88 |
<li> |
89 |
- <a href="http://celda.camplab.net/"> |
|
89 |
+ <a href="https://www.camplab.net/celda"> |
|
90 | 90 |
<span class="fas fa-home fa-lg"></span> |
91 | 91 |
|
92 | 92 |
</a> |
... | ... |
@@ -78,14 +78,14 @@ |
78 | 78 |
</button> |
79 | 79 |
<span class="navbar-brand"> |
80 | 80 |
<a class="navbar-link" href="../index.html">celda</a> |
81 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
81 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
82 | 82 |
</span> |
83 | 83 |
</div> |
84 | 84 |
|
85 | 85 |
<div id="navbar" class="navbar-collapse collapse"> |
86 | 86 |
<ul class="nav navbar-nav"> |
87 | 87 |
<li> |
88 |
- <a href="http://celda.camplab.net/"> |
|
88 |
+ <a href="https://www.camplab.net/celda"> |
|
89 | 89 |
<span class="fas fa-home fa-lg"></span> |
90 | 90 |
|
91 | 91 |
</a> |
... | ... |
@@ -357,7 +357,7 @@ is only used when `zInitialize = 'predfined'`. Default NULL.</p></td> |
357 | 357 |
K <span class='op'>=</span> <span class='va'>celdaCSim</span><span class='op'>$</span><span class='va'>K</span>, |
358 | 358 |
sampleLabel <span class='op'>=</span> <span class='va'>celdaCSim</span><span class='op'>$</span><span class='va'>sampleLabel</span>, |
359 | 359 |
nchains <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> |
360 |
-</div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Starting Celda_C: Clustering cells.</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:45 2021 .. Initializing 'z' in chain 1 with 'split' </span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:45 2021 .... Completed iteration: 1 | logLik: -1282027.27277705</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:45 2021 .... Completed iteration: 2 | logLik: -1282027.27277705</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:45 2021 .. Finished chain 1</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Completed Celda_C. Total time: 0.1618769 secs</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div></pre> |
|
360 |
+</div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Starting Celda_C: Clustering cells.</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:37 2021 .. Initializing 'z' in chain 1 with 'split' </span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:37 2021 .... Completed iteration: 1 | logLik: -1282027.27277705</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:37 2021 .... Completed iteration: 2 | logLik: -1282027.27277705</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:37 2021 .. Finished chain 1</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Completed Celda_C. Total time: 0.137078 secs</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div></pre> |
|
361 | 361 |
</div> |
362 | 362 |
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
363 | 363 |
<nav id="toc" data-toggle="toc" class="sticky-top"> |
... | ... |
@@ -78,14 +78,14 @@ |
78 | 78 |
</button> |
79 | 79 |
<span class="navbar-brand"> |
80 | 80 |
<a class="navbar-link" href="../index.html">celda</a> |
81 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
81 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
82 | 82 |
</span> |
83 | 83 |
</div> |
84 | 84 |
|
85 | 85 |
<div id="navbar" class="navbar-collapse collapse"> |
86 | 86 |
<ul class="nav navbar-nav"> |
87 | 87 |
<li> |
88 |
- <a href="http://celda.camplab.net/"> |
|
88 |
+ <a href="https://www.camplab.net/celda"> |
|
89 | 89 |
<span class="fas fa-home fa-lg"></span> |
90 | 90 |
|
91 | 91 |
</a> |
... | ... |
@@ -402,7 +402,7 @@ is only used when `zInitialize = 'predfined'`. Default NULL.</p></td> |
402 | 402 |
L <span class='op'>=</span> <span class='va'>celdaCGSim</span><span class='op'>$</span><span class='va'>L</span>, |
403 | 403 |
sampleLabel <span class='op'>=</span> <span class='va'>celdaCGSim</span><span class='op'>$</span><span class='va'>sampleLabel</span>, |
404 | 404 |
nchains <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> |
405 |
-</div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Starting Celda_CG: Clustering cells and genes.</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:46 2021 .. Initializing 'z' in chain 1 with 'split' </span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:46 2021 .. Initializing 'y' in chain 1 with 'split' </span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:49 2021 .... Completed iteration: 1 | logLik: -1215542.98684529</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:49 2021 .... Completed iteration: 2 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:49 2021 .... Completed iteration: 3 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:49 2021 .... Completed iteration: 4 | logLik: -1215542.98684529</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:49 2021 .... Completed iteration: 5 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... Completed iteration: 6 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... Completed iteration: 7 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... Completed iteration: 8 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... Completed iteration: 9 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... Determining if any gene clusters should be split.</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... No additional splitting was performed.</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... Determining if any cell clusters should be split.</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... No additional splitting was performed.</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... Completed iteration: 10 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... Determining if any cell clusters should be split.</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... No additional splitting was performed.</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .... Completed iteration: 11 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:50 2021 .. Finished chain 1</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Completed Celda_CG. Total time: 4.13753 secs</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div></pre> |
|
405 |
+</div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Starting Celda_CG: Clustering cells and genes.</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:38 2021 .. Initializing 'z' in chain 1 with 'split' </span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:38 2021 .. Initializing 'y' in chain 1 with 'split' </span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Completed iteration: 1 | logLik: -1215542.98684529</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Completed iteration: 2 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Completed iteration: 3 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Completed iteration: 4 | logLik: -1215542.98684529</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Completed iteration: 5 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Completed iteration: 6 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Completed iteration: 7 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Completed iteration: 8 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Completed iteration: 9 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Determining if any gene clusters should be split.</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... No additional splitting was performed.</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Determining if any cell clusters should be split.</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... No additional splitting was performed.</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Completed iteration: 10 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Determining if any cell clusters should be split.</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... No additional splitting was performed.</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .... Completed iteration: 11 | logLik: -1215541.0958389</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .. Finished chain 1</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Completed Celda_CG. Total time: 3.250677 secs</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div></pre> |
|
406 | 406 |
</div> |
407 | 407 |
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
408 | 408 |
<nav id="toc" data-toggle="toc" class="sticky-top"> |
... | ... |
@@ -78,14 +78,14 @@ |
78 | 78 |
</button> |
79 | 79 |
<span class="navbar-brand"> |
80 | 80 |
<a class="navbar-link" href="../index.html">celda</a> |
81 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
81 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
82 | 82 |
</span> |
83 | 83 |
</div> |
84 | 84 |
|
85 | 85 |
<div id="navbar" class="navbar-collapse collapse"> |
86 | 86 |
<ul class="nav navbar-nav"> |
87 | 87 |
<li> |
88 |
- <a href="http://celda.camplab.net/"> |
|
88 |
+ <a href="https://www.camplab.net/celda"> |
|
89 | 89 |
<span class="fas fa-home fa-lg"></span> |
90 | 90 |
|
91 | 91 |
</a> |
... | ... |
@@ -341,7 +341,7 @@ Default NULL.</p></td> |
341 | 341 |
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
342 | 342 |
<pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>celdaGSim</span><span class='op'>)</span> |
343 | 343 |
<span class='va'>sce</span> <span class='op'><-</span> <span class='fu'>celda_G</span><span class='op'>(</span><span class='va'>celdaGSim</span><span class='op'>$</span><span class='va'>counts</span>, L <span class='op'>=</span> <span class='va'>celdaGSim</span><span class='op'>$</span><span class='va'>L</span>, nchains <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> |
344 |
-</div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Starting Celda_G: Clustering genes.</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:51 2021 .. Initializing 'y' in chain 1 with 'split' </span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Completed iteration: 1 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Completed iteration: 2 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Completed iteration: 3 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Completed iteration: 4 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Completed iteration: 5 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Completed iteration: 6 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Completed iteration: 7 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Completed iteration: 8 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Completed iteration: 9 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Determining if any gene clusters should be split.</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... No additional splitting was performed.</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Completed iteration: 10 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .... Completed iteration: 11 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:53 2021 .. Finished chain 1</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Completed Celda_G. Total time: 2.769402 secs</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div></pre> |
|
344 |
+</div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Starting Celda_G: Clustering genes.</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:41 2021 .. Initializing 'y' in chain 1 with 'split' </span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:43 2021 .... Completed iteration: 1 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:43 2021 .... Completed iteration: 2 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:43 2021 .... Completed iteration: 3 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:43 2021 .... Completed iteration: 4 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:43 2021 .... Completed iteration: 5 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:43 2021 .... Completed iteration: 6 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:43 2021 .... Completed iteration: 7 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:44 2021 .... Completed iteration: 8 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:44 2021 .... Completed iteration: 9 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:44 2021 .... Determining if any gene clusters should be split.</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:44 2021 .... No additional splitting was performed.</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:44 2021 .... Completed iteration: 10 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:44 2021 .... Completed iteration: 11 | logLik: -290669.046132139</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:44 2021 .. Finished chain 1</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Completed Celda_G. Total time: 2.44341 secs</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div></pre> |
|
345 | 345 |
</div> |
346 | 346 |
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |
347 | 347 |
<nav id="toc" data-toggle="toc" class="sticky-top"> |
... | ... |
@@ -76,14 +76,14 @@ |
76 | 76 |
</button> |
77 | 77 |
<span class="navbar-brand"> |
78 | 78 |
<a class="navbar-link" href="../index.html">celda</a> |
79 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
79 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
80 | 80 |
</span> |
81 | 81 |
</div> |
82 | 82 |
|
83 | 83 |
<div id="navbar" class="navbar-collapse collapse"> |
84 | 84 |
<ul class="nav navbar-nav"> |
85 | 85 |
<li> |
86 |
- <a href="http://celda.camplab.net/"> |
|
86 |
+ <a href="https://www.camplab.net/celda"> |
|
87 | 87 |
<span class="fas fa-home fa-lg"></span> |
88 | 88 |
|
89 | 89 |
</a> |
... | ... |
@@ -77,14 +77,14 @@ |
77 | 77 |
</button> |
78 | 78 |
<span class="navbar-brand"> |
79 | 79 |
<a class="navbar-link" href="../index.html">celda</a> |
80 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
80 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
81 | 81 |
</span> |
82 | 82 |
</div> |
83 | 83 |
|
84 | 84 |
<div id="navbar" class="navbar-collapse collapse"> |
85 | 85 |
<ul class="nav navbar-nav"> |
86 | 86 |
<li> |
87 |
- <a href="http://celda.camplab.net/"> |
|
87 |
+ <a href="https://www.camplab.net/celda"> |
|
88 | 88 |
<span class="fas fa-home fa-lg"></span> |
89 | 89 |
|
90 | 90 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ in single cell genomic datasets." /> |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -387,7 +387,7 @@ cell cluster labels will be stored in |
387 | 387 |
#> <span class='message'></span> |
388 | 388 |
#> <span class='message'> anyMissing, rowMedians</span></div><div class='input'><span class='va'>sce</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>counts <span class='op'>=</span> <span class='va'>s</span><span class='op'>$</span><span class='va'>observedCounts</span><span class='op'>)</span><span class='op'>)</span> |
389 | 389 |
<span class='va'>sce</span> <span class='op'><-</span> <span class='fu'>decontX</span><span class='op'>(</span><span class='va'>sce</span><span class='op'>)</span> |
390 |
-</div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Starting DecontX</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:56 2021 .. Analyzing all cells</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:56 2021 .... Converting to sparse matrix</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:24:57 2021 .... Generating UMAP and estimating cell types</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:25:00 2021 .... Estimating contamination</span></div><div class='output co'>#> <span class='message'>Wed Sep 29 12:25:00 2021 ...... Completed iteration: 9 | converge: 0.0009154</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Completed DecontX. Total time: 3.44309 secs</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='input'> |
|
390 |
+</div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Starting DecontX</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:46 2021 .. Analyzing all cells</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:46 2021 .... Converting to sparse matrix</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:46 2021 .... Generating UMAP and estimating cell types</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:49 2021 .... Estimating contamination</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:49 2021 ...... Completed iteration: 9 | converge: 0.0009154</span></div><div class='output co'>#> <span class='message'>Mon Oct 4 12:07:49 2021 .. Calculating final decontaminated matrix</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='output co'>#> <span class='message'>Completed DecontX. Total time: 2.786641 secs</span></div><div class='output co'>#> <span class='message'>--------------------------------------------------</span></div><div class='input'> |
|
391 | 391 |
<span class='co'># Plot contamination on UMAP</span> |
392 | 392 |
<span class='fu'><a href='plotDecontXContamination.html'>plotDecontXContamination</a></span><span class='op'>(</span><span class='va'>sce</span><span class='op'>)</span> |
393 | 393 |
</div><div class='img'><img src='decontX-1.png' alt='' width='700' height='433' /></div><div class='input'> |
... | ... |
@@ -73,14 +73,14 @@ a SingleCellExperiment object." /> |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -75,14 +75,14 @@ |
75 | 75 |
</button> |
76 | 76 |
<span class="navbar-brand"> |
77 | 77 |
<a class="navbar-link" href="../index.html">celda</a> |
78 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
78 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
79 | 79 |
</span> |
80 | 80 |
</div> |
81 | 81 |
|
82 | 82 |
<div id="navbar" class="navbar-collapse collapse"> |
83 | 83 |
<ul class="nav navbar-nav"> |
84 | 84 |
<li> |
85 |
- <a href="http://celda.camplab.net/"> |
|
85 |
+ <a href="https://www.camplab.net/celda"> |
|
86 | 86 |
<span class="fas fa-home fa-lg"></span> |
87 | 87 |
|
88 | 88 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -72,14 +72,14 @@ |
72 | 72 |
</button> |
73 | 73 |
<span class="navbar-brand"> |
74 | 74 |
<a class="navbar-link" href="../index.html">celda</a> |
75 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
75 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
76 | 76 |
</span> |
77 | 77 |
</div> |
78 | 78 |
|
79 | 79 |
<div id="navbar" class="navbar-collapse collapse"> |
80 | 80 |
<ul class="nav navbar-nav"> |
81 | 81 |
<li> |
82 |
- <a href="http://celda.camplab.net/"> |
|
82 |
+ <a href="https://www.camplab.net/celda"> |
|
83 | 83 |
<span class="fas fa-home fa-lg"></span> |
84 | 84 |
|
85 | 85 |
</a> |
... | ... |
@@ -74,14 +74,14 @@ |
74 | 74 |
</button> |
75 | 75 |
<span class="navbar-brand"> |
76 | 76 |
<a class="navbar-link" href="../index.html">celda</a> |
77 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
77 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
78 | 78 |
</span> |
79 | 79 |
</div> |
80 | 80 |
|
81 | 81 |
<div id="navbar" class="navbar-collapse collapse"> |
82 | 82 |
<ul class="nav navbar-nav"> |
83 | 83 |
<li> |
84 |
- <a href="http://celda.camplab.net/"> |
|
84 |
+ <a href="https://www.camplab.net/celda"> |
|
85 | 85 |
<span class="fas fa-home fa-lg"></span> |
86 | 86 |
|
87 | 87 |
</a> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |
... | ... |
@@ -75,14 +75,14 @@ |
75 | 75 |
</button> |
76 | 76 |
<span class="navbar-brand"> |
77 | 77 |
<a class="navbar-link" href="../index.html">celda</a> |
78 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
78 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
79 | 79 |
</span> |
80 | 80 |
</div> |
81 | 81 |
|
82 | 82 |
<div id="navbar" class="navbar-collapse collapse"> |
83 | 83 |
<ul class="nav navbar-nav"> |
84 | 84 |
<li> |
85 |
- <a href="http://celda.camplab.net/"> |
|
85 |
+ <a href="https://www.camplab.net/celda"> |
|
86 | 86 |
<span class="fas fa-home fa-lg"></span> |
87 | 87 |
|
88 | 88 |
</a> |
... | ... |
@@ -71,14 +71,14 @@ |
71 | 71 |
</button> |
72 | 72 |
<span class="navbar-brand"> |
73 | 73 |
<a class="navbar-link" href="../index.html">celda</a> |
74 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
74 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
75 | 75 |
</span> |
76 | 76 |
</div> |
77 | 77 |
|
78 | 78 |
<div id="navbar" class="navbar-collapse collapse"> |
79 | 79 |
<ul class="nav navbar-nav"> |
80 | 80 |
<li> |
81 |
- <a href="http://celda.camplab.net/"> |
|
81 |
+ <a href="https://www.camplab.net/celda"> |
|
82 | 82 |
<span class="fas fa-home fa-lg"></span> |
83 | 83 |
|
84 | 84 |
</a> |
... | ... |
@@ -413,7 +413,7 @@ |
413 | 413 |
<p><code><a href="celdaClusters.html">celdaClusters()</a></code> <code><a href="celdaClusters.html">`celdaClusters<-`()</a></code> </p> |
414 | 414 |
</td> |
415 | 415 |
<td><p>Get or set the cell cluster labels from a celda |
416 |
- <a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a> object or celda model |
|
416 |
+ SingleCellExperiment object or celda model |
|
417 | 417 |
object.</p></td> |
418 | 418 |
</tr><tr> |
419 | 419 |
|
... | ... |
@@ -421,7 +421,7 @@ |
421 | 421 |
<p><code><a href="celdaModules.html">celdaModules()</a></code> <code><a href="celdaModules.html">`celdaModules<-`()</a></code> </p> |
422 | 422 |
</td> |
423 | 423 |
<td><p>Get or set the feature module labels from a celda |
424 |
- <a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a> object.</p></td> |
|
424 |
+ SingleCellExperiment object.</p></td> |
|
425 | 425 |
</tr><tr> |
426 | 426 |
|
427 | 427 |
<td> |
... | ... |
@@ -552,7 +552,7 @@ |
552 | 552 |
<p><code><a href="sampleLabel.html">sampleLabel()</a></code> <code><a href="sampleLabel.html">`sampleLabel<-`()</a></code> </p> |
553 | 553 |
</td> |
554 | 554 |
<td><p>Get or set sample labels from a celda |
555 |
- <a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a> object</p></td> |
|
555 |
+ SingleCellExperiment object</p></td> |
|
556 | 556 |
</tr> |
557 | 557 |
</tbody><tbody> |
558 | 558 |
<tr> |
... | ... |
@@ -73,14 +73,14 @@ |
73 | 73 |
</button> |
74 | 74 |
<span class="navbar-brand"> |
75 | 75 |
<a class="navbar-link" href="../index.html">celda</a> |
76 |
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span> |
|
76 |
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span> |
|
77 | 77 |
</span> |
78 | 78 |
</div> |
79 | 79 |
|
80 | 80 |
<div id="navbar" class="navbar-collapse collapse"> |
81 | 81 |
<ul class="nav navbar-nav"> |
82 | 82 |
<li> |
83 |
- <a href="http://celda.camplab.net/"> |
|
83 |
+ <a href="https://www.camplab.net/celda"> |
|
84 | 84 |
<span class="fas fa-home fa-lg"></span> |
85 | 85 |
|
86 | 86 |
</a> |