freepluslq's Stars
cozygene/bisque
An R toolkit for estimation of cell composition from bulk expression data
scverse/scanpy
Single-cell analysis in Python. Scales to >1M cells.
dpeerlab/Palantir
Single cell trajectory detection
pachterlab/kallisto
Near-optimal RNA-Seq quantification
QuKunLab/APEC
Single cell epigenomic clustering based on accessibility pattern
QuKunLab/ATAC-pipe
Analysis pipeline for ATAC-seq Data
lmcinnes/umap
Uniform Manifold Approximation and Projection
sandhya212/BISCUIT_SingleCell_IMM_ICML_2016
R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.
AllonKleinLab/SPRING_dev
freepluslq/ATAC-pipe
Analysis pipeline for ATAC-seq Data
seandavi/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
satijalab/seurat
R toolkit for single cell genomics
bmvdgeijn/WASP
WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery