project

Ultrafast GPU-enabled QTL mapper

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

R package for integrating and analyzing multiple single-cell datasets

Code for Walker, Saunders, Rai et al., (2021).

Links to ATAC-seq analysis tools

Imputation of parental genotypes, inference of sibling IBD segments, family based GWAS, and polygenic score analyses.

Documentation for the ANNOVAR software

Code for creating cell-type-specific regulatory element annotation files

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines

Repo for the R package coloc

A modular, containerized pipeline for PRO-seq data processing

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool

ATAC-seq and DNase-seq processing pipeline

scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources…

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries

Annotated data.

A modular, containerized pipeline for ATAC-seq data processing

Customizable workflows based on snakemake and python for the analysis of NGS data

Project metadata manager for PEPs in Python

Differential expression analysis for single-cell RNA-seq data.

Python toolkit for building restartable pipelines

This Snakemake pipeline implements the GATK best-practices workflow