1. celda
  2. Commit 7c5d27c94b7fd8d305138d64ad96537926f2a8d6
Browse code

Updated version, docs, nav bar, and NEWS

Joshua D. Campbell authored on 04/10/2021 16:44:28
Showing 118 changed files
DESCRIPTION
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 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.9.2
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+Version: 1.9.3
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
NEWS.md
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+# celda v1.9.3 (2021-10-04)
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+
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 * Fixed bug in checking background matrix with decontX
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 * Switched to using Github Actions for Continuous Integration
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 * Fixed plotting bugs in celda results reports
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+* Speed up final step in decontX when creating final decontaminated matrix
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 # celda v1.9.2 (2021-07-19)
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_pkgdown.yml
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   - plotDecontXContamination
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   - plotDecontXMarkerExpression
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   - plotDecontXMarkerPercentage
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+
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   - decontXcounts
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 - title: Functions for determining the numbers of clusters in celda
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   title: "celda"
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   left:
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     - icon: fa-home fa-lg
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-      href: http://celda.camplab.net/
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+      href: https://www.camplab.net/celda
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     - text: "Installation"
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       href: articles/articles/installation.html
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     - text: "Vignettes"
docs/404.html
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="index.html">celda</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
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       </span>
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     <div id="navbar" class="navbar-collapse collapse">
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       <ul class="nav navbar-nav">
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         <li>
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   </a>
docs/CONDUCT.html
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         <a class="navbar-link" href="index.html">celda</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
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     <div id="navbar" class="navbar-collapse collapse">
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       <ul class="nav navbar-nav">
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         <li>
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docs/LICENSE-text.html
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="index.html">celda</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="../../index.html">celda</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.2</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.9.3</span>
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       <h1 data-toc-skip>Celda - Analysis of PBMC3K</h1>
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                         <h4 class="author">Joshua Campbell, Zhe Wang</h4>
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-            <h4 class="date">Compiled September 29, 2021</h4>
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       <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>
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 ## other attached packages:
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 ##  [1] scater_1.18.6               kableExtra_1.3.4
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 ##  [3] knitr_1.31                  ggplot2_3.3.5
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 ##  [7] TENxPBMCData_1.8.0          HDF5Array_1.18.1
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 ##  [9] rhdf5_2.34.0                DelayedArray_0.16.2
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 ## [11] Matrix_1.3-2                SingleCellExperiment_1.12.0
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       <h1 data-toc-skip>DecontX - Decontamination of PBMC4K</h1>
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                         <h4 class="author">Joshua Campbell, Shiyi Yang, Zhe Wang, Yuan Yin</h4>
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 ## [11] GenomicRanges_1.42.0        GenomeInfoDb_1.26.4
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 ## [13] IRanges_2.24.1              S4Vectors_0.28.1
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 ## [15] BiocGenerics_0.36.0         MatrixGenerics_1.2.1
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 ## loaded via a namespace (and not attached):
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 ##   [1] AnnotationHub_2.22.0          BiocFileCache_1.14.0
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             <address class="author_afil">
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       Boston University School of Medicine<br><h4 class="author">Yusuke Koga</h4>
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+<li>Switched to using Github Actions for Continuous Integration</li>
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+<li>Fixed plotting bugs in celda results reports</li>
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+<li>Speed up final step in decontX when creating final decontaminated matrix</li>
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+<h1 class="page-header" data-toc-text="1.0.1">
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+<h1 class="page-header" data-toc-text="0.99.34">
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+</ul>
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+</div>
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+    <div id="celda-v09923-2019-04-10" class="section level1">
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+<h1 class="page-header" data-toc-text="0.99.23">
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+</ul>
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+    <div id="celda-v09922-2019-04-09" class="section level1">
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+<h1 class="page-header" data-toc-text="0.99.22">
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+<a href="#celda-v09922-2019-04-09" class="anchor"></a>celda v0.99.22 (2019-04-09):</h1>
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+<ul>
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+</ul>
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+    <div id="celda-v0998-2019-03-11" class="section level1">
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+<h1 class="page-header" data-toc-text="0.99.8">
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+</div>
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+    <div id="celda-v0990-2018-05-15" class="section level1">
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+<h1 class="page-header" data-toc-text="0.99.0">
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     K <span class='op'>=</span> <span class='va'>celdaCSim</span><span class='op'>$</span><span class='va'>K</span>,
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-</div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Starting Celda_C: Clustering cells.</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Wed Sep 29 12:24:45 2021 .. Initializing 'z' in chain 1 with 'split' </span></div><div class='output co'>#&gt; <span class='message'>Wed Sep 29 12:24:45 2021 .... Completed iteration: 1 | logLik: -1282027.27277705</span></div><div class='output co'>#&gt; <span class='message'>Wed Sep 29 12:24:45 2021 .... Completed iteration: 2 | logLik: -1282027.27277705</span></div><div class='output co'>#&gt; <span class='message'>Wed Sep 29 12:24:45 2021 .. Finished chain 1</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Completed Celda_C. Total time: 0.1618769 secs</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div></pre>
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     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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     <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>celdaGSim</span><span class='op'>)</span>
343 343 
 <span class='va'>sce</span> <span class='op'>&lt;-</span> <span class='fu'>celda_G</span><span class='op'>(</span><span class='va'>celdaGSim</span><span class='op'>$</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>
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+</div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Starting Celda_G: Clustering genes.</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:41 2021 .. Initializing 'y' in chain 1 with 'split' </span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:43 2021 .... Completed iteration: 1 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:43 2021 .... Completed iteration: 2 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:43 2021 .... Completed iteration: 3 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:43 2021 .... Completed iteration: 4 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:43 2021 .... Completed iteration: 5 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:43 2021 .... Completed iteration: 6 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:43 2021 .... Completed iteration: 7 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:44 2021 .... Completed iteration: 8 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:44 2021 .... Completed iteration: 9 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:44 2021 .... Determining if any gene clusters should be split.</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:44 2021 .... No additional splitting was performed.</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:44 2021 .... Completed iteration: 10 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:44 2021 .... Completed iteration: 11 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Mon Oct  4 12:07:44 2021 .. Finished chain 1</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Completed Celda_G. Total time: 2.44341 secs</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div></pre>
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     <span class="fas fa-home fa-lg"></span>
85 85
86 86 
   </a>
docs/reference/logLikelihoodHistory.html
History View file @ 7c5d27c9
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@@ -73,14 +73,14 @@
73