ccrobertson

ccrobertson's Stars

• bigdatagenomics/adam

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

  Language:Scala1k1001.2k308

• scverse/anndata

  Annotated data.

  Language:Python57814734152

• welch-lab/liger

  R package for integrating and analyzing multiple single-cell datasets

  Language:R3892218978

• maxplanck-ie/snakepipes

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

  Language:Python3832047085

• snakemake-workflows/dna-seq-gatk-variant-calling

  This Snakemake pipeline implements the GATK best-practices workflow

  Language:Python242926147

• WGLab/doc-ANNOVAR

  Documentation for the ANNOVAR software

  23225246353

• PacificBiosciences/FALCON

  FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries

  Language:Python20554586102

• theislab/diffxpy

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

  Language:Python192718823

• molgenis/systemsgenetics

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

  Language:Java1714794100

• kundajelab/atac_dnase_pipelines

  ATAC-seq and DNase-seq processing pipeline

  Language:Python1624813581

• broadinstitute/tensorqtl

  Ultrafast GPU-enabled QTL mapper

  Language:Python1601415352

• chr1swallace/coloc

  Repo for the R package coloc

  Language:R146414944

• PMBio/scLVM

  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 of variation.

  Language:HTML104192746

• databio/pepatac

  A modular, containerized pipeline for ATAC-seq data processing

  Language:R542224414

• databio/awesome-atac-analysis

  Links to ATAC-seq analysis tools

  492006

• HumanCellAtlas/skylab

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

  Language:WDL47232734

• databio/pypiper

  Python toolkit for building restartable pipelines

  Language:Python46161689

• statgen/popscle

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

  Language:C++4397315

• pepkit/peppy

  Project metadata manager for PEPs in Python

  Language:Python37430713

• AlexTISYoung/snipar

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

  Language:Python232195

• immunogenomics/IMPACT

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

  Language:R181288

• databio/peppro

  A modular, containerized pipeline for PRO-seq data processing

  Language:Python1014802

• ParkerLab/2021_islet-rfx6

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

  Language:Roff2300

• porchard/wf-single-cell

  Language:Python1000