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XingyanLiu · Jun 9, 2022 · d337eda · d337eda
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diff --git a/README.md b/README.md
@@ -97,8 +97,11 @@ We have a mailing list located at:
 
 Citation
 --------
-If you find StagewiseNN helps, Please cite:
+If you find StagewiseNN helps, please cite:
 
-> Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al. 
+> Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al.,
 > **Joint profiling of gene expression and chromatin accessibility of amphioxus 
-> development at single cell resolution**, 18 May 2021, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-504113/v1]
+> development at single-cell resolution**,
+> _Cell Reports_ (2022), https://doi.org/10.1016/j.celrep.2022.110979
+
+<img src="docs/source/_figs/graphic_summ.png" height="400"/>
diff --git a/docs/_sources/citation.rst.txt b/docs/_sources/citation.rst.txt
@@ -1,9 +1,9 @@
 Citation
 ========
 
-If you find StagewiseNN helps, Please cite:
+If you find StagewiseNN helps, please cite:
 
-   Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al.
+   Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al.,
    **Joint profiling of gene expression and chromatin accessibility of amphioxus
-   development at single cell resolution**, 18 May 2021, PREPRINT (Version 1)
-   available at Research Square [https://doi.org/10.21203/rs.3.rs-504113/v1]
+   development at single-cell resolution**,
+   Cell Reports (2022), https://doi.org/10.1016/j.celrep.2022.110979
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
@@ -7,11 +7,11 @@ StagewiseNN - Building developmental tree from single-cell data
 ===============================================================
 
 **StagewiseNN** is a computational tool for constructing
-developmental (lineage) tree from Multi-staged single-cell RNA-seq data.
+developmental (lineage) tree from multi-staged single-cell RNA-seq data.
 
 It starts from building a single-cell graph by connecting each cell to its
-k-nearest neighbors in the parent stage, followed by voting-based tree-construction
-and adaptive cluster refinement.
+k-nearest neighbors in the parent stage, followed by the voting-based tree-construction
+and an adaptive cluster refinement.
 
 .. image:: _figs/swnn_overview.png
    :height: 300px

diff --git a/docs/build/doctrees/citation.doctree b/docs/build/doctrees/citation.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/html/_sources/citation.rst.txt b/docs/build/html/_sources/citation.rst.txt
@@ -1,9 +1,9 @@
 Citation
 ========
 
-If you find StagewiseNN helps, Please cite:
+If you find StagewiseNN helps, please cite:
 
-   Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al.
+   Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al.,
    **Joint profiling of gene expression and chromatin accessibility of amphioxus
-   development at single cell resolution**, 18 May 2021, PREPRINT (Version 1)
-   available at Research Square [https://doi.org/10.21203/rs.3.rs-504113/v1]
+   development at single-cell resolution**,
+   Cell Reports (2022), https://doi.org/10.1016/j.celrep.2022.110979
diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
@@ -7,11 +7,11 @@ StagewiseNN - Building developmental tree from single-cell data
 ===============================================================
 
 **StagewiseNN** is a computational tool for constructing
-developmental (lineage) tree from Multi-staged single-cell RNA-seq data.
+developmental (lineage) tree from multi-staged single-cell RNA-seq data.
 
 It starts from building a single-cell graph by connecting each cell to its
-k-nearest neighbors in the parent stage, followed by voting-based tree-construction
-and adaptive cluster refinement.
+k-nearest neighbors in the parent stage, followed by the voting-based tree-construction
+and an adaptive cluster refinement.
 
 .. image:: _figs/swnn_overview.png
    :height: 300px

diff --git a/docs/build/html/citation.html b/docs/build/html/citation.html
@@ -186,12 +186,12 @@
 </style>
 <div class="section" id="citation">
 <h1>Citation<a class="headerlink" href="#citation" title="Permalink to this headline">¶</a></h1>
-<p>If you find StagewiseNN helps, Please cite:</p>
+<p>If you find StagewiseNN helps, please cite:</p>
 <blockquote>
-<div><p>Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al.
+<div><p>Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al.,
 <strong>Joint profiling of gene expression and chromatin accessibility of amphioxus
-development at single cell resolution</strong>, 18 May 2021, PREPRINT (Version 1)
-available at Research Square [<a class="reference external" href="https://doi.org/10.21203/rs.3.rs-504113/v1">https://doi.org/10.21203/rs.3.rs-504113/v1</a>]</p>
+development at single-cell resolution</strong>,
+Cell Reports (2022), <a class="reference external" href="https://doi.org/10.1016/j.celrep.2022.110979">https://doi.org/10.1016/j.celrep.2022.110979</a></p>
 </div></blockquote>
 </div>
 

diff --git a/docs/build/html/index.html b/docs/build/html/index.html
@@ -187,10 +187,10 @@
 <div class="section" id="stagewisenn-building-developmental-tree-from-single-cell-data">
 <h1>StagewiseNN - Building developmental tree from single-cell data<a class="headerlink" href="#stagewisenn-building-developmental-tree-from-single-cell-data" title="Permalink to this headline">¶</a></h1>
 <p><strong>StagewiseNN</strong> is a computational tool for constructing
-developmental (lineage) tree from Multi-staged single-cell RNA-seq data.</p>
+developmental (lineage) tree from multi-staged single-cell RNA-seq data.</p>
 <p>It starts from building a single-cell graph by connecting each cell to its
-k-nearest neighbors in the parent stage, followed by voting-based tree-construction
-and adaptive cluster refinement.</p>
+k-nearest neighbors in the parent stage, followed by the voting-based tree-construction
+and an adaptive cluster refinement.</p>
 <a class="reference internal image-reference" href="_images/swnn_overview.png"><img alt="_images/swnn_overview.png" src="_images/swnn_overview.png" style="height: 300px;" /></a>
 <p>The single-cell graph can be further visualized using graph embedding methods, e.g. UMAP, SPRING.</p>
 <p>We have used it to build the developmental tree from the <strong>snRNA-seq</strong> of amphioxus embryonic cells, across

diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
diff --git a/docs/citation.html b/docs/citation.html
@@ -186,12 +186,12 @@
 </style>
 <div class="section" id="citation">
 <h1>Citation<a class="headerlink" href="#citation" title="Permalink to this headline">¶</a></h1>
-<p>If you find StagewiseNN helps, Please cite:</p>
+<p>If you find StagewiseNN helps, please cite:</p>
 <blockquote>
-<div><p>Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al.
+<div><p>Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al.,
 <strong>Joint profiling of gene expression and chromatin accessibility of amphioxus
-development at single cell resolution</strong>, 18 May 2021, PREPRINT (Version 1)
-available at Research Square [<a class="reference external" href="https://doi.org/10.21203/rs.3.rs-504113/v1">https://doi.org/10.21203/rs.3.rs-504113/v1</a>]</p>
+development at single-cell resolution</strong>,
+Cell Reports (2022), <a class="reference external" href="https://doi.org/10.1016/j.celrep.2022.110979">https://doi.org/10.1016/j.celrep.2022.110979</a></p>
 </div></blockquote>
 </div>
 

diff --git a/docs/index.html b/docs/index.html
@@ -187,10 +187,10 @@
 <div class="section" id="stagewisenn-building-developmental-tree-from-single-cell-data">
 <h1>StagewiseNN - Building developmental tree from single-cell data<a class="headerlink" href="#stagewisenn-building-developmental-tree-from-single-cell-data" title="Permalink to this headline">¶</a></h1>
 <p><strong>StagewiseNN</strong> is a computational tool for constructing
-developmental (lineage) tree from Multi-staged single-cell RNA-seq data.</p>
+developmental (lineage) tree from multi-staged single-cell RNA-seq data.</p>
 <p>It starts from building a single-cell graph by connecting each cell to its
-k-nearest neighbors in the parent stage, followed by voting-based tree-construction
-and adaptive cluster refinement.</p>
+k-nearest neighbors in the parent stage, followed by the voting-based tree-construction
+and an adaptive cluster refinement.</p>
 <a class="reference internal image-reference" href="_images/swnn_overview.png"><img alt="_images/swnn_overview.png" src="_images/swnn_overview.png" style="height: 300px;" /></a>
 <p>The single-cell graph can be further visualized using graph embedding methods, e.g. UMAP, SPRING.</p>
 <p>We have used it to build the developmental tree from the <strong>snRNA-seq</strong> of amphioxus embryonic cells, across

diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/docs/source/_figs/graphic_summ.png b/docs/source/_figs/graphic_summ.png
diff --git a/docs/source/citation.rst b/docs/source/citation.rst
@@ -1,9 +1,9 @@
 Citation
 ========
 
-If you find StagewiseNN helps, Please cite:
+If you find StagewiseNN helps, please cite:
 
-   Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al.
+   Pengcheng Ma, Xingyan Liu, Zaoxu Xu et al.,
    **Joint profiling of gene expression and chromatin accessibility of amphioxus
-   development at single cell resolution**, 18 May 2021, PREPRINT (Version 1)
-   available at Research Square [https://doi.org/10.21203/rs.3.rs-504113/v1]
+   development at single-cell resolution**,
+   Cell Reports (2022), https://doi.org/10.1016/j.celrep.2022.110979