deploy: 1f52ac3

Author: scverse-bot

packages/index.html

@@ -49,7 +49,7 @@
 <span class=package-details>decoupler is a framework containing different enrichment statistical methods to extract biologically driven scores from omics data within a unified framework.</span></div></div><div class=package-links><a href=https://github.com/scverse/decoupler target=_blank>GitHub</a>
 <a href=https://decoupler.readthedocs.io/en/latest/ target=_blank>Documentation and tutorials</a>
 <a href=https://pypi.org/project/decoupler/ target=_blank>PyPI</a>
-<a href=https://anaconda.org/conda-forge/decoupler-py target=_blank>Conda</a></div></div></div></div><h2 id=ecosystem>Ecosystem packages maintained by scverse community</h2><div><p><p>Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).</p><p><em>This listing is a work in progress. See <a href=https://github.com/scverse/ecosystem-packages>scverse/ecosystem-packages</a> for inclusion criteria, and to submit more packages.</em></p></p></div><div id=ecosystem-packages><input type=text class=form-control id=eco-filter onkeyup=filterPackages() placeholder="Search through 107 packages" title="Type in your search query"><table class=table id=eco-table><thead><tr><th scope=col>Package</th><th scope=col>Description</th></tr></thead><tbody><tr class="package-links eco-table-row"><td><a href=https://github.com/quadbio/cell-annotator target=_blank>CellAnnotator</a></td><td>CellAnnotator is a lightweight tool to query large language models for cell type labels in scRNA-seq data. It can incorporate prior knowledge, and it creates consistent labels across samples in your study.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/CSOgroup/cellcharter target=_blank>CellCharter</a></td><td>CellCharter is a framework to identify, characterize and compare spatial domains from spatial omics and multi-omics data.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/quadbio/cellmapper target=_blank>CellMapper</a></td><td>CellMapper is a leightweight tool to transfer labels, expression values and embeddings from reference to query datasets using k-NN mapping. It&rsquo;s fast and versatile, applicable to mapping scenarios in space, across modalities, or from an atlas to a new query dataset.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/morris-lab/CellOracle target=_blank>CellOracle</a></td><td>A computational tool that integrates single-cell transcriptome and epigenome profiles
+<a href=https://anaconda.org/conda-forge/decoupler-py target=_blank>Conda</a></div></div></div></div><h2 id=ecosystem>Ecosystem packages maintained by scverse community</h2><div><p><p>Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).</p><p><em>This listing is a work in progress. See <a href=https://github.com/scverse/ecosystem-packages>scverse/ecosystem-packages</a> for inclusion criteria, and to submit more packages.</em></p></p></div><div id=ecosystem-packages><input type=text class=form-control id=eco-filter onkeyup=filterPackages() placeholder="Search through 108 packages" title="Type in your search query"><table class=table id=eco-table><thead><tr><th scope=col>Package</th><th scope=col>Description</th></tr></thead><tbody><tr class="package-links eco-table-row"><td><a href=https://github.com/quadbio/cell-annotator target=_blank>CellAnnotator</a></td><td>CellAnnotator is a lightweight tool to query large language models for cell type labels in scRNA-seq data. It can incorporate prior knowledge, and it creates consistent labels across samples in your study.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/CSOgroup/cellcharter target=_blank>CellCharter</a></td><td>CellCharter is a framework to identify, characterize and compare spatial domains from spatial omics and multi-omics data.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/quadbio/cellmapper target=_blank>CellMapper</a></td><td>CellMapper is a leightweight tool to transfer labels, expression values and embeddings from reference to query datasets using k-NN mapping. It&rsquo;s fast and versatile, applicable to mapping scenarios in space, across modalities, or from an atlas to a new query dataset.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/morris-lab/CellOracle target=_blank>CellOracle</a></td><td>A computational tool that integrates single-cell transcriptome and epigenome profiles
 to infer gene regulatory networks (GRNs), critical regulators of cell identity.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/theislab/cellrank target=_blank>CellRank</a></td><td>CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data.
 It contains two main modules - kernels compute cell-cell transition probabilities and estimators generate
 hypothesis based on these.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/gao-lab/Cell_BLAST target=_blank>Cell_BLAST</a></td><td>Cell BLAST is a cell querying tool for single-cell transcriptomics data.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/ventolab/CellphoneDB target=_blank>CellphoneDB</a></td><td>CellphoneDB is a publicly available repository of HUMAN curated receptors, ligands and their interactions paired with a tool to interrogate your own single-cell transcriptomics data (or even bulk transcriptomics data if your samples represent pure populations!). A distinctive feature of CellphoneDB is that the subunit architecture of either ligands and receptors is taken into account, representing heteromeric complexes accurately. This is crucial, as cell communication relies on multi-subunit protein complexes that go beyond the binary representation used in most databases and studies. CellphoneDB also incorporates biosynthetic pathways in which we use the last representative enzyme as a proxy of ligand abundance, by doing so, we include interactions involving non-peptidic molecules. CellphoneDB includes only manually curated and reviewed molecular interactions with evidenced role in cellular communication.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/lilab-bcb/cirrocumulus target=_blank>Cirrocumulus</a></td><td>Cirrocumulus is an interactive visualization tool for large-scale single-cell genomics data.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/theislab/DRVI target=_blank>DRVI</a></td><td>DRVI is a tool for the unsupervised disentanglement and integration of single-cell omics.
@@ -94,7 +94,7 @@
 Analyze high-dimensional cytometry data using FlowSOM,
 a clustering and visualization algorithm based on a self-organizing map (SOM).
 FlowSOM is used to distinguish cell populations from cytometry data in an unsupervised way and
-can help to gain deeper insights in fields such as immunology and oncology.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/scverse/governance target=_blank>governance</a></td><td>Governance docs for scverse</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/IlyaLab/gssnng target=_blank>gssnng</a></td><td>Single-cell gene set scoring with nearest neighbor graph smoothed data.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/yoseflab/hotspot target=_blank>hotspot</a></td><td>Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/icbi-lab/infercnvpy target=_blank>infercnvpy</a></td><td>Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/scverse/integration-testing target=_blank>integration-testing</a></td><td>A repo for integration testing core packages against upstream core packages</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/settylab/kompot target=_blank>kompot</a></td><td>Statistical framework for holistic comparison of multi-condition single-cell datasets over continuous phenotypic manifolds.
+can help to gain deeper insights in fields such as immunology and oncology.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/scverse/governance target=_blank>governance</a></td><td>Governance docs for scverse</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/IlyaLab/gssnng target=_blank>gssnng</a></td><td>Single-cell gene set scoring with nearest neighbor graph smoothed data.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/yoseflab/hotspot target=_blank>hotspot</a></td><td>Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/remydubois/illico target=_blank>illico</a></td><td>illico runs fast, CPU-based, wilcoxon rank-sum tests to identify differentially expressed genes for single-cell RNA-seq data.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/icbi-lab/infercnvpy target=_blank>infercnvpy</a></td><td>Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/scverse/integration-testing target=_blank>integration-testing</a></td><td>A repo for integration testing core packages against upstream core packages</td></tr><tr class="package-links eco-table-row"><td><a href=https://github.com/settylab/kompot target=_blank>kompot</a></td><td>Statistical framework for holistic comparison of multi-condition single-cell datasets over continuous phenotypic manifolds.
 Kompot performs differential abundance and expression analysis agnostically to cell-type annotation or clustering,
 detecting differences that span the continuous manifold even when effects go in opposite directions across cell states.
 It models cell distributions and gene expression as continuous functions over cell state representations of arbitrary

people/index.html

@@ -149,6 +149,7 @@
 <a href=https://github.com/IsaacUtah1379 target=_blank>Isaac E.</a>,
 <a href=https://github.com/pjb7687 target=_blank>Jeongbin Park</a>,
 <a href=https://github.com/Sonja-Stockhaus target=_blank>Sonja-Stockhaus</a>,
+<a href=https://github.com/LiudengZhang target=_blank>LiudengZhang</a>,
 <a href=https://github.com/yfarjoun target=_blank>Yossi Farjoun</a>,
 <a href=https://github.com/maximz target=_blank>Maxim Zaslavsky</a>,
 <a href=https://github.com/MLubetzki target=_blank>MLubetzki</a>,
@@ -160,13 +161,13 @@
 <a href=https://github.com/roryk target=_blank>Rory Kirchner</a>,
 <a href=https://github.com/briangottfried target=_blank>Brian</a>,
 <a href=https://github.com/fionahamey target=_blank>fionahamey</a>,
-<a href=https://github.com/LucasESBS target=_blank>LucaSC</a>,
-<a href=https://github.com/LouisFaure target=_blank>LouisFaure</a>,
-<a href=https://github.com/LisaSikkema target=_blank>Lisa Sikkema</a>,
-<a href=https://github.com/jlause target=_blank>Jan Lause</a>,
 <a href=https://github.com/Iwo-K target=_blank>Iwo Kucinski</a>,
-<a href=https://github.com/swstkm target=_blank>Swastik Mishra</a>,
+<a href=https://github.com/jlause target=_blank>Jan Lause</a>,
+<a href=https://github.com/LisaSikkema target=_blank>Lisa Sikkema</a>,
+<a href=https://github.com/LouisFaure target=_blank>LouisFaure</a>,
+<a href=https://github.com/LucasESBS target=_blank>LucaSC</a>,
 <a href=https://github.com/stephenwilliams22 target=_blank>Stephen Williams</a>,
+<a href=https://github.com/swstkm target=_blank>Swastik Mishra</a>,
 <a href=https://github.com/mbuttner target=_blank>Maren Büttner</a>,
 <a href=https://github.com/marcovarrone target=_blank>Marco</a>,
 <a href=https://github.com/FrancescaDr target=_blank>Francesca Drummer</a>,
@@ -203,31 +204,30 @@
 <a href=https://github.com/DiDeoxy target=_blank>Max Hargreaves</a>,
 <a href=https://github.com/m-albert target=_blank>Marvin Albert</a>,
 <a href=https://github.com/MSHelm target=_blank>Martin Helm</a>,
-<a href=https://github.com/LiudengZhang target=_blank>LiudengZhang</a>,
 <a href=https://github.com/jlr13 target=_blank>Jan Lukas Rinker</a>,
 <a href=https://github.com/Czaki target=_blank>Grzegorz Bokota</a>,
 <a href=https://github.com/FloWuenne target=_blank>Florian Wuennemann</a>,
 <a href=https://github.com/EliHei2 target=_blank>Elyas Heidari</a>,
 <a href=https://github.com/dylanclam12 target=_blank>Dylan Lam</a>,
 <a href=https://github.com/clwgg target=_blank>Clemens Weiss</a>,
 <a href=https://github.com/Bisho2122 target=_blank>Bishoy Wadie</a>,
-<a href=https://github.com/Wainberg target=_blank>Wainberg</a>,
-<a href=https://github.com/VladimirShitov target=_blank>Vladimir Shitov</a>,
-<a href=https://github.com/vishnumenon target=_blank>Vishnu</a>,
-<a href=https://github.com/umangv target=_blank>Umang Varma</a>,
-<a href=https://github.com/timrandg target=_blank>Tim Rand</a>,
-<a href=https://github.com/Steve-Cheney target=_blank>Steve Cheney</a>,
-<a href=https://github.com/sshen8 target=_blank>Simon P Shen</a>,
-<a href=https://github.com/zeehio target=_blank>Sergio Oller</a>,
 <a href=https://github.com/senbaikang target=_blank>Senbai Kang</a>,
+<a href=https://github.com/zeehio target=_blank>Sergio Oller</a>,
+<a href=https://github.com/sshen8 target=_blank>Simon P Shen</a>,
+<a href=https://github.com/Steve-Cheney target=_blank>Steve Cheney</a>,
+<a href=https://github.com/timrandg target=_blank>Tim Rand</a>,
+<a href=https://github.com/umangv target=_blank>Umang Varma</a>,
+<a href=https://github.com/vishnumenon target=_blank>Vishnu</a>,
+<a href=https://github.com/VladimirShitov target=_blank>Vladimir Shitov</a>,
+<a href=https://github.com/stuartarchibald target=_blank>stuartarchibald</a>,
 <a href=https://github.com/slobentanzer target=_blank>Sebastian Lobentanzer</a>,
 <a href=https://github.com/RohanDisa target=_blank>Rohan Disa</a>,
 <a href=https://github.com/coh-racng target=_blank>Rachel Ng</a>,
 <a href=https://github.com/qianggong11 target=_blank>Qiang Gong</a>,
 <a href=https://github.com/padix-key target=_blank>Patrick Kunzmann</a>,
 <a href=https://github.com/PGmajev target=_blank>PGmajev</a>,
 <a href=https://github.com/noamteyssier target=_blank>Noam Teyssier</a>,
-<a href=https://github.com/stuartarchibald target=_blank>stuartarchibald</a>,
+<a href=https://github.com/mxposed target=_blank>Nick Markov</a>,
 <a href=https://github.com/snigdhaAgarwal target=_blank>snigdhaAgarwal</a>,
 <a href=https://github.com/smautner target=_blank>smautner</a>,
 <a href=https://github.com/thetorpedodog target=_blank>paul fisher</a>,
@@ -247,6 +247,7 @@
 <a href=https://github.com/Zaf4 target=_blank>Zafer Kosar</a>,
 <a href=https://github.com/Yves33 target=_blank>Yves33</a>,
 <a href=https://github.com/yuanx749 target=_blank>Xiao Yuan</a>,
+<a href=https://github.com/Wainberg target=_blank>Wainberg</a>,
 <a href=https://github.com/jhung0 target=_blank>Jane Hung</a>,
 <a href=https://github.com/iandriver target=_blank>Ian Driver</a>,
 <a href=https://github.com/gjeuken target=_blank>Gustavo Jeuken</a>,
@@ -267,7 +268,6 @@
 <a href=https://github.com/AminAlam target=_blank>Amin Alam</a>,
 <a href=https://github.com/alexmascension target=_blank>Alex M. Ascensión</a>,
 <a href=https://github.com/LarytheLord target=_blank>Abi</a>,
-<a href=https://github.com/mxposed target=_blank>Nick Markov</a>,
 <a href=https://github.com/nchlis target=_blank>Nikolaos K. Chlis</a>,
 <a href=https://github.com/n-hackert target=_blank>Nicolaj Hackert</a>,
 <a href=https://github.com/mukundvarma target=_blank>Mukund Varma</a>,