chrisamiller

fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

readDepth

R package for inferring copy number from read depth

copyCat

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

docker-genomic-analysis

Basic docker image for ad-hoc genomic analyses

bioinfoSnippets

Short snippets of code useful for bioinformatics and genomics

docker-phlat

dockerization of phlat hla typing tool

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.

bedtools2

bedtools - the swiss army knife for genome arithmetic

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

cv

CV webpage

docker-abra

docker image for abra - Assembly Based ReAligner

docker-alignment_helper-cwl

docker-biscuit

Biscuit + htslib for bgzip

docker-bsseq-r

docker image for doing bsseq analysis in R

docker-cnvkit

docker-gatk

adding some deps to the gatk image

docker-gdc-client

docker image for running the gdc client

docker-homer

fork of the quay.io homer image, moving annotations to my hardcoded link

docker-how_stranded

docker for https://github.com/betsig/how_are_we_stranded_here

docker-pod5-tools

dockerization of pod5tools

docker-pvactools

docker-somatic-llr-filter

Container for the somatic-llr filter

docker-synapser

docker image for R synapser package

flair

Full-Length Alternative Isoform analysis of RNA

gatk4-data-processing

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

nextflow

A DSL for data-driven computational pipelines

sqanti3-docker

A docker image to run SQANTI3

wdl_samtools.manta

WDL workflow for identifying fusion sites from tumor BAMs