drmjc Goto Github PK

bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure

blat

An R package for I/O of UCSC BLAT data.

excelio

an R package for I/O of Microsoft Excel files

foreign

Modified or extracted from other programs

gatk-protected

GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only

gemini

a lightweight db framework for disease and population genetics.

genomics

An R package of code for genomics (mostly pre-NGS)

grabix

a wee tool for random access into BGZF files.

homebrew

The missing package manager for OS X.

homebrew-core

🍻 Default formulae for the missing package manager for macOS (or Linux)

homebrew-science

:microscope: Scientific formulae for the Homebrew package manager

lumidat

An R package for processing Illumina gene expression idat files

macsr

An R package for handling MACS (ChIP-Seq) result files

metagsea

An R package for I/O of GenePattern datatypes, and running meta-GSEA analyses

microarrays

An R package containing a collection of microarray and genomic helper code.

mitoseek

Seeking information like heteroplasmy, structure variants, etc. on Mitochondrial genome from next generation sequencing

mjcaffy

An R package for Affymetrix microarray data analysis

mjcbase

An R package of useful utilities that I find useful on a day to day basis.

mjcgraphics

An R package of graphics plots. Mostly base graphics for bioinformatics data

mjcstats

An R package of simple statistics code.

o8

Genetic changes we can believe in: a web based tool for variant visualization and analysis

paradigm

PAthway Representation and Analysis by Direct Inference on Graphical Models

relex

An R package Ting and Cowley et al, MCP 2019: Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling.

roxygen

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

sapphire-utils

drmjc's NHMRC Sapphire Utilities

scnaphase

Profile haploid somatic copy number alterations,especially for NGS sequencing data on significantly contaminated tumor samples

test_that

An R package to make testing fun

textmate_bundles

drmjc's textmate bundles

updater

An R package for rapid R package development. The workhorse is updateR.sh, which can roxygenize, build, install, testthat, and deploy