/snATACClusteringPipeline

Pipeline for obtaining clusters from snATAC-seq data.

Primary LanguageShellGNU General Public License v3.0GPL-3.0

snATACClusteringPipeline

Pipeline for obtain clusters from snATAC-seq data.

For now, this pipeline is an implementation of the method describe by Satpathy, A.T, Granja, J.M., et al. (2019).

Dependencies:

snATACClusteringTools: Obtain/Compile the jar from: https://github.com/UcarLab/snATACClusteringTools Place the jar in the same directory at the shell script.

R (Tested with verion 3.6.2) R Libraries:

  1. Seurat: https://cran.r-project.org/web/packages/Seurat/index.html
  2. EdgeR: https://bioconductor.org/packages/release/bioc/html/edgeR.html
  3. Matrix: https://cran.r-project.org/web/packages/Matrix/index.html
  4. matrixStats: https://cran.r-project.org/web/packages/matrixStats/index.html