Software

• ConDecon: an R package implementing a clustering-independent deconvolution method for estimating cell abundances in bulk tissues using single-cell RNA-seq data. [GitHub]

• CAJAL: a python library for integrative and multi-modal analyses of single-cell morphological data based on applied metric geometry. [GitHub]

• EPNClassifier: an R package that assigns ependymal tumors profiled by bulk transcriptomics into molecular subgroups. [GitHub]

• TDAmut: an R package for the identification of novel driver genes using TDA on TCGA data. [GitHub]

• STvEA: an R package for the analysis and integration of matching CODEX and CITE-seq data sets. [GitHub] [Docker]

• RayleighSelection: an R package for feature selection in topological spaces derived from point clouds. [GitHub] [Docker]

• scTDA: an object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data. [GitHub] [Docker]

• TARGet: topological inference of horizontal evolution from multiple sequence alignments. [GitHub]