Ben Weisburd's repositories
annotation-utils
misc. python utilities
step-pipeline
This library is a thin layer over Hail Batch that adds features like skipping steps whose output files have already been generated, additional options for localizing files, notifications on pipeline completion, etc.
ConfigArgParse
A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.
ExpansionHunter
A tool for estimating repeat sizes
perf
PERF is an Exhaustive Repeat Finder
Pangolin
Pangolin is a deep-learning method for predicting splice site strengths.
bin-utils
Misc. command line utils
popSTR
PopSTR - A Population based microsatellite genotyper
igv.js
Embeddable genomic visualization component based on the Integrative Genomics Viewer
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
hail-utils
misc. hail utils
deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
impute_sample_metadata
Hail Batch pipelines for imputing the reference genome version, sample type, etc. from BAM or CRAM files.
LIRICAL
LIkelihood Ratio Interpretation of Clinical AbnormaLities
phaser
phasing and Allele Specific Expression from RNA-seq
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
DeepTrio
DeepTrio tests
MAPS
code for computing MAPS scores
hail
Scalable genomic data analysis.
actions-gh-pages
GitHub Actions for GitHub Pages 🚀 Deploy static files and publish your site easily. Static-Site-Generators-friendly.
hail-scripts
hail scripts from misc. analyses
GangSTR
A tool for profiling long STRs from short reads
STRetch
Method for detecting STR expansions from short-read sequencing data