lbergelson

lbergelson's Stars

• Homebrew/brew

  🍺 The missing package manager for macOS (or Linux)

  Language:Ruby42k7284.6k9.9k

• rastapasta/mapscii

  🗺 MapSCII is a Braille & ASCII world map renderer for your console - enter => telnet mapscii.me <= on Mac (brew install telnet) and Linux, connect with PuTTY on Windows

  Language:JavaScript8k10776258

• xroche/coffeecatch

  CoffeeCatch, a tiny native POSIX signal catcher (especially useful for JNI code on Android/Dalvik)

  Language:C6875135135

• chrchang/plink-ng

  A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.

  Language:C42927246126

• tbroyer/gradle-errorprone-plugin-v0.0.x

  Gradle plugin to use the error-prone compiler for Java

  Language:Java346167319

• PapenfussLab/gridss

  GRIDSS: the Genomic Rearrangement IDentification Software Suite

  Language:Java2612266071

• mroth/evalcache

  :hatching_chick: zsh plugin to cache eval loads to improve shell startup time

  Language:Shell2045410

• sskorol/test-data-supplier

  TestNG DataProvider on steroids

  Language:Java145137224

• ssadedin/bazam

  A read extraction and realignment tool for next generation sequencing data

  Language:Groovy9963116

• softwaremill/maven-badges

  A node.js implementation of https://github.com/jirutka/maven-badges, originally created in ruby.

  Language:TypeScript87271318

• mikepenz/gradle-dependency-submission

  Calculates dependencies for a Gradle build-target and submits the list to the Dependency Submission API

  Language:TypeScript803021

• googleapis/java-storage-nio

  Language:Java714817133

• mlin/spVCF

  Sparse Project VCF: evolution of VCF to encode population genotype matrices efficiently

  Language:C++586171

• themadcreator/circle-github-bot

  CircleCI comments on github

  Language:TypeScript583714

• broadinstitute/cromshell

  CLI for interacting with Cromwell servers

  Language:Python532911515

• stjudecloud/oliver

  An opinionated Cromwell orchestration manager.

  Language:Python408134

• disq-bio/disq

  A library for manipulating bioinformatics sequencing formats in Apache Spark

  Language:Java31127711

• broadinstitute/palantir-workflows

  Utility workflows for the DSP hydro.gen team (formerly palantir)

  Language:WDL2211318

• mklarqvist/tachyon

  High-level API for storing and querying sequence variant data

  Language:C++20543

• broadinstitute/widdler

  A command-line tool for executing, managing, and querying WDL workflows on Cromwell servers.

  Language:Python132067

• ga4gh/htsget-refserver

  Reference server implementation for the GA4GH HTSget API standard.

  Language:Go11294

• broadinstitute/cromwell-task-monitor-bq

  Scalable reporting of Cromwell task call resource monitoring data to BigQuery

  Language:Go9812

• microsoft/mgl

  Microsoft Genomics Library contains highly optimized compute cores for genomics applications

  Language:C++81106

• samtools/htsjdk-next-beta

  Staging ground for the development of the next major version of HTSJDK

  Language:Java610233

• HumanCellAtlas/unity

  UNITY is a workflow benchmarking platform used for developing and comparing pipelines.

  Language:Ruby52621

• broadinstitute/gatk-tool-wdls

  Autogenerated WDLs for GATK Tools

  Language:WDL4303

• broadinstitute/homebrew-dsp

  A brew tap for tools and formula that DSP uses that aren't ready for publishing to homebrew-core

  Language:Ruby4910

• dalessioluca/cromwell_for_ML

  Examples of how to use cromwell to run ML model at scale

  Language:Jupyter Notebook3150

• lbergelson/http-nio

  **Under development** HTTP/S FileSystem provider for Java NIO.2

  Language:Java10

• RoriCremer/gatk

  Official code repository for GATK versions 4 and up

  Language:Java1