walaj Goto Github PK

apophenia-clone

Copy of distribution version of Apophenia, with added statistical models

aws-cli-user-guide

The open source version of the AWS CLI User Guide

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

bxtools

Tools for analyzing 10X Genomics data

carreview

Manubot CAR-T Review Paper

cycifr

R package for processing highly multiplexed spatial imaging data (e.g. CyCIF)

cyftools

CLI tools for CyCIF

cyslib

C library for high-throughput multiplex imaging data formats

cytif

Command line tools for image processing using libvips

encode-download

Download and process tracks from ENCODE

ensapi

Command-line interface to Ensembl REST API

fermi-lite

Standalone C library for assembling Illumina short reads in small regions

fishhook

R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

ginseng

Tools for 1D and 2D genomic significance analysis

gtrack

R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework

jutils

R utilities and shortcuts

kdtree

Simple C++ KD-Tree implementation

lattice

libtiff

OBSOLETE and not updated any more libtiff mirror, see website for the new one

ncbitax2lin

Convert NCBI taxonomy dump into lineages

pthread-lite

Light-weight header library for C++ concurrency with pthread

roverlaps

Fast and memory efficient genomic range overlaps for R

seqlib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

seqtools

Basic command-line sequence analysis utilities I can't find elsewhere

setup

Useful customizations of a unix environment

splitthreader

Explore rearrangements and copy-number amplifications in a cancer genome

svaba

Structural variation and indel detection by local assembly

svlib

Toolkit for extracting SVs from long sequences and benchmarking variant callers

svsig

Recurrent structural variations detection in cancer whole genomes