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feather

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

genome_info_curve

Genome Utility

ginkgo

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

hadoop-cluster

Documentation and scripts on the Langmed Lab Hadoop cluster at MARCC

hisat

Fast spliced aligner with low memory requirements

hisat2

Graph-based alignment (Hierarchical Graph FM index)

jhu-compute

Resources to help use JHU's compute resources

jhu_int_prog

Publicly visible materials for intermediate programming

jupyter-all

Jupyter environment with various language kernels already installed

kmc

Fast and frugal disk based k-mer counter

knitr-examples

a collection of knitr examples

kraken

Kraken taxonomic sequence classification system

kraken2

The second version of the Kraken taxonomic sequence classification system

kraken2-experiment-code

Code backing the results of the Kraken 2 paper

labby

Lab simulator

langmead-lab

Publicly-visible Langmead Lab resources

langmead-lab-web

Langmead lab website

mnms

moni

MONI: A Pangenomic Index for Finding MEMs

myrna

Cloud-scale differential expression for RNA-seq

open-data-registry

A registry of publicly available datasets on AWS

percy

Scripts for starting permanent, lightweight EC2 instances

pfbwt-f

Prefix Free Parsing Algorthim for building BWTs for genomic data

public-seq-data

Scripts, manifests, etc for grabbing and lightly analyzing public data

qtip

Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities

qtip-experiments

Experiments for the qsim manuscript

rail

Scalable RNA-seq analysis

recount

R package for the recount project

recount-docker

Dockerization of recount and its R/Bioconductor dependencies

recount.bwtool

Fast coverage matrices from recount data using bwtool