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allcools

Toolkit for single-cell DNA methylation analysis.

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

cemba_data

Mapping pipeline for snmC-seq based technologies.

dialogue

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.

echo

jupyter notebooks of the analysis in ECHO paper

epivia

Identify vector integration site with both bulk and single-cell epigenomic assays

sceqtl

Code for single-cell eQTL analysis of memory T cell data in Nathan, et al. bioRxiv (2021)

schicluster

singlecellnotes

Notes about single cell technology and computational analysis methods, including but not limitted to Genome, Epigenome, Transcriptome, Morphology, Connectome and the integrative analysis of information from these layers.

tcf-1