Ruismart

gatk

Official code repository for GATK versions 4 and up

seqtk

Toolkit for processing sequences in FASTA/Q formats

sci-CAR_analysis

Scripts for processing sci-RNA-seq/sci-ATAC-seq/sci-CAR reads processing

cicero

scater

Clone of the Bioconductor repository for the scater package.

wgsim

Reads simulator

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

scRNA.seq.datasets

Collection of public scRNA-Seq datasets used by our group

SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

scABC

htslib

C library for high-throughput sequencing data formats

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

patchelf

A small utility to modify the dynamic linker and RPATH of ELF executables

issues

Code Unrelated Issues

atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

nucseq_analysis

single nuclei RNA-seq analysis toolbox

cgmaptools

toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR

vnote

A pleasant note-taking platform.

seurat

R toolkit for single cell genomics

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

cufflinks

monocle-release