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ah_biopharma

BioPharma projects

analysis-wdls

Early stages of converting genome/analysis-workflows from CWL to WDL

analysis-workflows

MGI's Analysis Workflows and Pipelines managed by the BGA group.

bam-window

bam-window code for getting depth in genomic intervals

bedtools2

bedtools - the swiss army knife for genome arithmetic

bedtools_tutorials

bioinfosnippets

Short snippets of code useful for bioinformatics and genomics

biscuit

C tools for analyzing sodium bisulfite converted sequencing data

cdna_cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

cloud-workflows

Infrastructure and tooling required to get genomic workflows running in the cloud

commute-times

calculate drive times from multiple locations and visualize them in google earth

conics

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing

convertensemblgtf

Convert ensembl GTF from [1,2,3] nomenclature to [chr1, chr2, chr3] nomenclature

copycat

a parallel R package for detecting copy-number alterations from short sequencing reads

cv

CV webpage

davidapi

A ruby wrapper for a few of the DAVID API functions for functional gene annotation (http://david.abcc.ncifcrf.gov/)

docker-abra

docker image for abra - Assembly Based ReAligner

docker-alignment_helper-cwl

docker-bam_readcount_helper-cwl

docker-bamsurgeon

dockerfile for bamsurgeon

docker-bcftools

Docker container for bcftools

docker-biscuit

Biscuit + htslib for bgzip

docker-bisulfite

a fat pipeline for running WGBS analysis

docker-bsseq-r

docker image for doing bsseq analysis in R

docker-cellranger

docker-cle

Docker containerization for the CLE

docker-cnvkit

docker-copycat

docker image for the R copyCat package

docker-finger

finger command

docker-fp_filter-cwl