scfurl

henipipe

Pipeline for CnR, CnT

m3addon

mergeBams

Merge bam files with intelligent cell barcode preservation

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

piperna

Making bulk RNA seq analysis easier

seqGlue

viewmaster

AnnotationHub

Client for the Bioconductor AnnotationHub web resource

arrayfire

ChIPQC

CITE-seq-Count

A tool that allows to get UMI counts from a single cell protein assay

COMETSC

COMET Single-Cell Marker Detection tool

conga

Clonotype Neighbor Graph Analysis

data_etc

repo for some data files

differ

Differ is a rust library for finding the differences between two sequences.

kgraph

A library for k-nearest neighbor search

lassonet

Feature selection in neural networks

mutCaller

call mutations in 10X data

NHPTregIL2

Analysis of IL2 NHP Treg data

qsubr

rcpparrayfire

R and ArrayFire library via Rcpp

scATACutils

R/Bioconductor package for working with 10x scATACseq data

scCUT-Tag

scRepertoire

A toolkit for single-cell immune profiling

SEACR

SEACR: Sparse Enrichment Analysis for CUT&RUN

sinto

Tools for single-cell data processing

SnapTools

A module for working with snap files in Python

souporcell

Clustering scRNAseq by genotypes

Vennerable

Old code

WAT3R

Workflow for the Association of T-cell receptors from 3' single-cell RNA-seq (WAT3R)