chrisamiller

bioinfoSnippets

Short snippets of code useful for bioinformatics and genomics

commute-times

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

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

fishplot

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

igvScreenshot

Create static screenshots of genomic regions using IGV.

netChopScraper

Allows programmatic retrieval of peptide cleavage predictions from the NetChop server at http://www.cbs.dtu.dk/services/NetChop/

readDepth

R package for inferring copy number from read depth

RMEmod

A tool for discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors

rtm-cli

A command-line Remember the Milk client written in perl

chrisamiller/fishplot

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

chrisamiller/readDepth

R package for inferring copy number from read depth

chrisamiller/copyCat

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

chrisamiller/docker-genomic-analysis

Basic docker image for ad-hoc genomic analyses

chrisamiller/bioinfoSnippets

Short snippets of code useful for bioinformatics and genomics

chrisamiller/docker-phlat

dockerization of phlat hla typing tool

chrisamiller/analysis-wdls

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

chrisamiller/analysis-workflows

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

chrisamiller/bedtools2

bedtools - the swiss army knife for genome arithmetic

chrisamiller/cDNA_Cupcake

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

chrisamiller/cloud-workflows

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

chrisamiller/cv

CV webpage

chrisamiller/docker-abra

docker image for abra - Assembly Based ReAligner

chrisamiller/docker-alignment_helper-cwl

chrisamiller/docker-biscuit

Biscuit + htslib for bgzip

chrisamiller/docker-bsseq-r

docker image for doing bsseq analysis in R

chrisamiller/docker-cnvkit

chrisamiller/docker-gatk

adding some deps to the gatk image

chrisamiller/docker-gdc-client

docker image for running the gdc client

chrisamiller/docker-homer

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

chrisamiller/docker-how_stranded

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

chrisamiller/docker-pod5-tools

dockerization of pod5tools

chrisamiller/docker-pvactools

chrisamiller/docker-somatic-llr-filter

Container for the somatic-llr filter

chrisamiller/docker-synapser

docker image for R synapser package

chrisamiller/flair

Full-Length Alternative Isoform analysis of RNA

chrisamiller/gatk4-data-processing

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

chrisamiller/nextflow

A DSL for data-driven computational pipelines

chrisamiller/sqanti3-docker

A docker image to run SQANTI3

chrisamiller/wdl_samtools.manta

WDL workflow for identifying fusion sites from tumor BAMs