{"id":254,"date":"2022-10-30T00:25:46","date_gmt":"2022-10-30T00:25:46","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/yuanlab\/?page_id=254"},"modified":"2025-04-10T18:30:14","modified_gmt":"2025-04-10T18:30:14","slug":"software","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/yuanlab\/software\/","title":{"rendered":"Software"},"content":{"rendered":"<ul>\n<li>ONTraC: A Tool for niche trajectory analysis using spatial omics data.<\/li>\n<\/ul>\n<p>[ <a href=\"https:\/\/ontrac-website.readthedocs.io\/\">Link to website<\/a> ] [ <a href=\"https:\/\/github.com\/gyuanlab\/ONTraC\">Link to GitHub<\/a> ]<\/p>\n<ul>\n<li><b>Giotto: A comprehensive toolbox for spatial multi-omic data analysis.\u00a0<\/b><\/li>\n<\/ul>\n<blockquote><p>[<a href=\"https:\/\/labs.icahn.mssm.edu\/yuanlab\/giotto\/\"> Link to Giotto Page<\/a> ]<\/p><\/blockquote>\n<ul>\n<li><b>DWLS: Cell-type deconvolution by using single-cell RNA-sequencing data.<\/b><\/li>\n<\/ul>\n<blockquote><p>[<a href=\"https:\/\/cran.rstudio.com\/web\/packages\/DWLS\/index.html\"> Link to CRAN<\/a> ]<\/p><\/blockquote>\n<ul>\n<li><b>CUT&amp;RUNTools: Analyzing CUT&amp;RUN and CUT&amp;Tag data.\u00a0<\/b><\/li>\n<\/ul>\n<blockquote><p><a href=\"https:\/\/bitbucket.org\/qzhudfci\/cutruntools\">[ Version 1<\/a>\u00a0(bulk analysis); <a href=\"https:\/\/github.com\/fl-yu\/CUT-RUNTools-2.0\">Version 2<\/a> (single-cell analysis) ]<\/p><\/blockquote>\n<ul>\n<li><b>GiniClust: Detection of rare cell-types from single-cell RNAseq data.\u00a0<\/b><\/li>\n<\/ul>\n<blockquote><p><a href=\"https:\/\/github.com\/lanjiangboston\/GiniClust\">[ Version 1<\/a>; <a href=\"https:\/\/github.com\/dtsoucas\/GiniClust2\">Version 2<\/a>; <a href=\"https:\/\/github.com\/rdong08\/GiniClust3\/\">Version 3<\/a> ]<\/p><\/blockquote>\n<ul>\n<li><b>diHMM: Multi-scale chromatin state annotation from ChIPseq data.<\/b><\/li>\n<\/ul>\n<blockquote><p>[<a href=\"https:\/\/github.com\/gcyuan\/diHMM\/\">Link to GitHub<\/a>].<\/p><\/blockquote>\n<ul>\n<li><b>CRISPResso: Analyzing deep-sequencing CRISPR-Cas9 genome editing outcome data<\/b><\/li>\n<\/ul>\n<blockquote><p>[<a href=\"https:\/\/github.com\/lucapinello\/CRISPResso\">Link to GitHub<\/a>]<\/p><\/blockquote>\n<ul>\n<li><b>SCUBA: Trajectory and bifurcation analysis of single-cell RNAseq data<\/b><\/li>\n<\/ul>\n<blockquote><p>[<a href=\"https:\/\/github.com\/gcyuan\/SCUBA\/\">Link to GitHub<\/a>]<\/p><\/blockquote>\n<ul>\n<li><b>STREAM: Pseudotime and trajectory analysis from single-cell RNAseq or ATACseq data.<\/b><\/li>\n<\/ul>\n<blockquote><p>[<a href=\"http:\/\/stream.pinellolab.org\/\">\u00a0Link to Website\u00a0<\/a>]<\/p><\/blockquote>\n<ul>\n<li><b>RESCUE: Imputing dropouts in single-cell RNA-sequencing data.<\/b><\/li>\n<\/ul>\n<blockquote><p>[<a href=\"https:\/\/github.com\/seasamgo\/rescue\"> Link to GitHub <\/a>]<\/p><\/blockquote>\n<ul>\n<li><b>Haystack: Quantifying chromatin state variability and prediction of driving transcription factors<\/b><\/li>\n<\/ul>\n<blockquote><p>[\u00a0<a href=\"https:\/\/github.com\/pinellolab\/haystack_bio\">Link to Github\u00a0<\/a>]<\/p><\/blockquote>\n<ul>\n<li><b>PANDA: Constructing gene regulatory network from RNA, TF motif, and PPI data\u00a0<\/b><\/li>\n<\/ul>\n<blockquote><p>[<a href=\"https:\/\/netzoo.github.io\/zooanimals\/panda\/\">Link to Website<\/a>]<\/p><\/blockquote>\n<ul>\n<li><b>MAnorm: a robust model for quantitative comparison of ChIP-seq datasets<\/b><\/li>\n<\/ul>\n<blockquote><p>[<a href=\"https:\/\/manorm.readthedocs.io\/en\/latest\/\">Link to Website<\/a>]<\/p><\/blockquote>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>ONTraC: A Tool for niche trajectory analysis using spatial omics data. [ Link to website ] [ Link to GitHub ] Giotto: A comprehensive toolbox for spatial multi-omic data analysis.\u00a0 [ Link to Giotto Page ] DWLS: Cell-type deconvolution by using single-cell RNA-sequencing data. [ Link to CRAN ] CUT&amp;RUNTools: Analyzing CUT&amp;RUN and CUT&amp;Tag data.\u00a0 [&hellip;]<\/p>\n","protected":false},"author":443,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-254","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/yuanlab\/wp-json\/wp\/v2\/pages\/254","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/yuanlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/yuanlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/yuanlab\/wp-json\/wp\/v2\/users\/443"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/yuanlab\/wp-json\/wp\/v2\/comments?post=254"}],"version-history":[{"count":11,"href":"https:\/\/labs.icahn.mssm.edu\/yuanlab\/wp-json\/wp\/v2\/pages\/254\/revisions"}],"predecessor-version":[{"id":363,"href":"https:\/\/labs.icahn.mssm.edu\/yuanlab\/wp-json\/wp\/v2\/pages\/254\/revisions\/363"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/yuanlab\/wp-json\/wp\/v2\/media?parent=254"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}