An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

This list of writing prompts covers a range of topics and tasks, including brainstorming research ideas, improving language and style, conducting literature reviews, and developing research plans.

A structural variation pipeline for short-read sequencing

Nextflow pipeline for performing parallel alternative splicing analysis using rMATS and Whippet and then overlapping the results.

a fully Bayesian approach to deconvolve tumor microenvironment

Tutorial for scRNA-seq data analysis beginners using R

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)

A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter)

Code to run OncoSig Analyses

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Analysis pipeline for cancer exomes

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

Various utility tools for working with genomics data

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

C library for high-throughput sequencing data formats

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

Tools (written in C using htslib) for manipulating next-generation sequencing data

A powerful toolset for genome arithmetic.

Statistical Rethinking course at MPI-EVA from Dec 2018 through Feb 2019

Batch effect adjustment based on negative binomial regression for RNA sequencing count data

parallel fastq-dump wrapper

optimized protocol for processing 50-bp SE ChIP-seq

DriverML identifies cancer driver genes. Rigorous and unbiased benchmark analysis and comparisons of DriverML with 20 other existing tools in 31 independent datasets from The Cancer Genome Atlas (T…

QuPath - Open Source Digital Pathology

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

immunarch: An R Package for Painless Bioinformatics Analysis of T-cell and B-cell Immune Repertoire Data

Docker container for JDownloader 2

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.