Garrett Graham's repositories
AECT
A deep learning based pipeline for TSS coverage denoising and feature extraction from shallow cell free DNA sequencing
autoconf-archive
A mirror of the GNU Autoconf Archive, a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet.
bax2bam
Convert legacy PacBio Bax.H5, Bas.H5, and Ccs.H5 files to the new PacBio BAM format
MACS
MACS -- Model-based Analysis of ChIP-Seq
pbbam
PacBio BAM C++ library
BBHash
Bloom-filter based minimal perfect hash function library
bpRNA
bpRNA: Large-scale Annotation and Analysis of RNA Secondary Structure
bwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
cuttlefish
Building the compacted de Bruijn graph efficiently from references or reads.
deepTools
Tools to process and analyze deep sequencing data.
fermi-lite
Standalone C library for assembling Illumina short reads in small regions
ggh4x
ggplot extension: options for tailored facets, multiple colourscales and miscellaneous
Griffin
A flexible framework for nucleosome profiling of cell-free DNA
hisat2
Graph-based alignment (Hierarchical Graph FM index) (SIMDe)
KMC
Fast and frugal disk based k-mer counter
memes
An R interface to the MEME Suite
MethylDackel
A (mostly) universal methylation extractor for BS-seq experiments.
nim-lapper
fast easy interval overlapping for nim-lang
paragraph
Graph realignment tools for structural variants
pbcopper
Core C++ library for data structures, algorithms, and utilities
Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
wensn
Python library to read the Wensn WS1361 Sound Pressure Level Meter over USB (on the Raspberry Pi)
WiggleTools
Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency