Tools we are developing can be found on our GitHub page: https://github.com/UcarLab

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• IA-SVA: A statistical framework to detect unwanted heterogeneity in single-cell RNA-seq datasets. A statistical method to uncover hidden and correlated sources of variation from single cell RNA-seq data.     

             Source code, Bioconductor R package​, Manuscript, R Shiny App

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• QUIN: A query tool to build chromatin, annotate and query chromatin interaction networks. A web server for Querying and Visualizing Chromatin Interaction Networks. QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license. 

             Source code, ​Web server, Manuscript  ​​

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• BiFET: an enrichment test for TF footprinting analyses. A test designed to reduce the false positive enrichments in TF footprinting analyses. ​

             Source code, Bioconductor R package, Manuscript

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• PEAS: Predicting enhancers from ATAC-seq: A neural network method to predict enhancers from ATAC-seq data an enrichment test for TF footprinting analyses. 

             Source code, Manuscript          

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