BenLangmead

bowtie-scaling

Experiments for "Scaling read aligners to hundreds of threads on general-purpose processors"

bioconda-recipes

Conda recipes for the bioconda channel.

sra-example

bowtie-dev

docker-oss

Automatic compatibility tests, e.g. to learn which OS versions a binary can be run on

hisat

Fast spliced aligner with low memory requirements

hisat2

Graph-based alignment (Hierarchical Graph FM index)

KMC

Fast and frugal disk based k-mer counter

snaptron

fast webservices based query tool for large sets of genomic features

bounter

Efficient Counter that uses a limited (bounded) amount of memory regardless of data size.

bowtie-site

Files behind the Bowtie website

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

bwtool

A tool for bigWig files.

circleci-test

cloud-review

feather

Feather: fast, interoperable binary data frame storage for Python, R, and more powered by Apache Arrow

ginkgo

Cloud-based single-cell copy-number variation analysis tool

hadoop-cluster

Documentation and scripts on the Langmed Lab Hadoop cluster at MARCC

jhu_int_prog

Publicly visible materials for intermediate programming

knitr-examples

a collection of knitr examples

mnms

qtip-experiments

Experiments for the qsim manuscript

rail

Scalable RNA-seq analysis

recount

R package for the recount project

recount.bwtool

Fast coverage matrices from recount data using bwtool

singularity-test

Simple tests to see how image URLs map onto branches, tags, hashes and commits in Singularity Hub

squeakr

Squeakr: An Exact and Approximate k -mer Counting System

stepik-experiments

Example code for interacting with Stepik API

stringtie

Transcript assembly and quantification for RNA-Seq

vagrant-docker

Containers with vagrant and libraries needed to run on EC2