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annotation-utils

misc. python utilities

bin-utils

Misc. command line utils

bw2.github.io

configargparse

A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.

deeptrio

DeepTrio tests

deepvariant

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

expansionhunter

A tool for estimating repeat sizes

fraser

gangstr

A tool for profiling long STRs from short reads

hail

Scalable genomic data analysis.

hail-scripts

hail scripts from misc. analyses

hail-utils

misc. hail utils

httpd-echo

A Simple Python HTTP server that echos the request in the response

igv.js

Embeddable genomic visualization component based on the Integrative Genomics Viewer

impute_sample_metadata

Hail Batch pipelines for imputing the reference genome version, sample type, etc. from BAM or CRAM files.

kubernetes-elasticsearch-cluster

Elasticsearch cluster on top of Kubernetes made easy.

lirical

LIkelihood Ratio Interpretation of Clinical AbnormaLities

maps

code for computing MAPS scores

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

pangolin

Pangolin is a deep-learning method for predicting splice site strengths.

perf

PERF is an Exhaustive Repeat Finder

phaser

phasing and Allele Specific Expression from RNA-seq

popstr

PopSTR - A Population based microsatellite genotyper

process_profiler

Runs in the background and records telemetry on running processes and system resources. Designed for instrumenting jobs in compute clusters.

pycircos

python Circos

pypez

simple pipelines in python

reviewer

A tool for visualizing alignments of reads in regions containing tandem repeats

rnaseq-viewer

sma_carrier_detection