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bsub

python wrapper to submit jobs to bsub (and later qsub)

bw-python

python wrapper to dpryan79's bigwig library using cffi

bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

bwa-mips

Map sequence from Molecular Inversion Probes with BWA, strip arms, de-dup, ..., profit

c-blosc2

A simple, compressed, fast and persistent data store library for C

cabage-manuscript

celltypes450

adjust for cell-type composition in 450K data using houseman's and other methods.

cgotabix

quick-n-dirty tabix in go using cgo

cgotbx

yeah, another tabix wrapper for go.

chroma

Everything you want to do with colors, in nim.

cigar

simple library for dealing with SAM cigar strings

clinical-components

Summarize the clinical (or lab) components and correlations of your dataset.

clustermodel

fitting models to clustered correlated data

clustermodelr

fit models to clustered, correlated data (R package)

cnvkit

Copy number variant detection from targeted DNA sequencing

cnvnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

combat.py

python / numpy / pandas / patsy version of ComBat for removing batch effects.

combined-pvalues

combining p-values using modified stouffer-liptak for spatially correlated results (probes)

conda

OS-agnostic, system-level binary package manager and ecosystem

covviz

Multi-sample genome coverage viewer to observe large, coverage-based anomalies

cqf-nim

nim wrapper for counting quotient filter

crampex

cram reader in golang via system call to samtools

cruzdb

python access to UCSC genomes database

crystal

find clusters and model correlated data from DNA methylation and other genomic sources.

cysolar

copy of pysolar using cython

cyvcf2

cython + htslib == fast VCF and BCF processing

d4-format

The D4 Quantitative Data Format

d4-nim

nim-lang wrapper for https://github.com/38/d4-format

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.