Awesome Single CellCommunity-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Stars: ✭ 1,937 (+12006.25%)
Mutual labels: atac-seq, single-cell
single-cell-papers-with-codePapers with code for single cell related papers
Stars: ✭ 20 (+25%)
Mutual labels: single-cell, single-cell-atac-seq
gchromVARCell type specific enrichments using finemapped variants and quantitative epigenetic data
Stars: ✭ 31 (+93.75%)
Mutual labels: atac-seq, single-cell
scATAC-proA comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
Stars: ✭ 63 (+293.75%)
Mutual labels: atac-seq, single-cell
pyflow-ATACseqATAC-seq snakemake pipeline
Stars: ✭ 61 (+281.25%)
Mutual labels: atac-seq
ATAC-seqBasic workflow for ATAC-seq analysis
Stars: ✭ 30 (+87.5%)
Mutual labels: atac-seq
scCATCHAutomatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
Stars: ✭ 137 (+756.25%)
Mutual labels: single-cell
cnaCovarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.
Stars: ✭ 35 (+118.75%)
Mutual labels: single-cell
SpiceMixspatial transcriptome, single cell
Stars: ✭ 19 (+18.75%)
Mutual labels: single-cell
iDEADifferential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
Stars: ✭ 23 (+43.75%)
Mutual labels: single-cell
ATACseqAnalysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
Stars: ✭ 51 (+218.75%)
Mutual labels: atac-seq
NucleoATACnucleosome calling using ATAC-seq
Stars: ✭ 95 (+493.75%)
Mutual labels: atac-seq
scATAC-benchmarkingBenchmarking computational single cell ATAC-seq methods
Stars: ✭ 137 (+756.25%)
Mutual labels: atac-seq
GGR-cwlCWL tools and workflows for GGR
Stars: ✭ 20 (+25%)
Mutual labels: atac-seq
ataqvA toolkit for QC and visualization of ATAC-seq results.
Stars: ✭ 55 (+243.75%)
Mutual labels: atac-seq
cellrangerRkitNon-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)
Stars: ✭ 18 (+12.5%)
Mutual labels: single-cell
scDblFinderMethods for detecting doublets in single-cell sequencing data
Stars: ✭ 48 (+200%)
Mutual labels: single-cell
PandoMultiome GRN inference.
Stars: ✭ 21 (+31.25%)
Mutual labels: single-cell
crop-seqData analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)
Stars: ✭ 24 (+50%)
Mutual labels: single-cell
OrchestratingSingleCellAnalysis-releaseAn online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.
Stars: ✭ 35 (+118.75%)
Mutual labels: single-cell
