Browse code

Updated version, docs, nav bar, and NEWS

Joshua D. Campbell authored on 04/10/2021 16:44:28
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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")),
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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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   - 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"
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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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       </span>
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       </button>
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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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       </button>
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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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       </button>
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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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+            <h4 class="date">Compiled October 04, 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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-##  [5] celda_1.9.2                 singleCellTK_2.2.0         
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+##  [5] celda_1.9.3                 singleCellTK_2.2.0         
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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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       </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>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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-            <h4 class="date">Compiled September 29, 2021</h4>
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+            <h4 class="date">Compiled October 04, 2021</h4>
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       <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>
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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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 ## 
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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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-        <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">1.9.2</span>
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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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             <address class="author_afil">
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-      Boston University School of Medicine<br><h4 class="date">2021-09-29</h4>
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+      Boston University School of Medicine<br><h4 class="date">2021-10-04</h4>
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 ##  [5] GenomeInfoDb_1.26.4         IRanges_2.24.1             
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       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>
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       </address>
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 ## [11] GenomicRanges_1.42.0        GenomeInfoDb_1.26.4        
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       <small>Source: <a href='https://github.com/campbio/celda/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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 <li>Minor bug fix when the input matrix was sparse and contained non-integer values.</li>
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+    <div id="celda-v174-2021-03-09" class="section level1">
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+<a href="#celda-v116-2019-07-16" class="anchor"></a>celda v1.1.6 (2019-07-16):</h1>
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+    <div id="celda-v101-2019-05-09" class="section level1">
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+<h1 class="page-header" data-toc-text="1.0.1">
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+    <div id="celda-v09934-2019-04-23" class="section level1">
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+<h1 class="page-header" data-toc-text="0.99.34">
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+<h1 class="page-header" data-toc-text="0.99.23">
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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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+    <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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+<a href="#celda-v0998-2019-03-11" class="anchor"></a>celda v0.99.8 (2019-03-11):</h1>
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+<ul>
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+</ul>
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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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     <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>
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 <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 DecontX</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Wed Sep 29 12:24:56 2021 .. Analyzing all cells</span></div><div class='output co'>#&gt; <span class='message'>Wed Sep 29 12:24:56 2021 .... Converting to sparse matrix</span></div><div class='output co'>#&gt; <span class='message'>Wed Sep 29 12:24:57 2021 .... Generating UMAP and estimating cell types</span></div><div class='output co'>#&gt; <span class='message'>Wed Sep 29 12:25:00 2021 .... Estimating contamination</span></div><div class='output co'>#&gt; <span class='message'>Wed Sep 29 12:25:00 2021 ...... Completed iteration: 9 | converge: 0.0009154</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Completed DecontX. Total time: 3.44309 secs</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='input'>
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