Pinned Repositories
barclay
Command line argument parser and online documentation generation utilities for java command line programs.
gatk
Official code repository for GATK versions 4 and up
gatk-bwamem-jni
JNI code for bwa mem
gatk-native-bindings
GATK Native Bindings Repository
jopt-simple
Java library for parsing command line options
variant-to-igv
A tool which takes a variant file and bams, and creates igv screenshots of each of the variants.
htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
lbergelson's Repositories
lbergelson/bioconda-recipes
Conda recipes for the bioconda channel.
lbergelson/brew
🍺 The missing package manager for macOS
lbergelson/coffeecatch
CoffeeCatch, a tiny native POSIX signal catcher (especially useful for JNI code on Android/Dalvik)
lbergelson/course-v3
The 3rd edition of course.fast.ai
lbergelson/DataflowTemplates
Google-provided Cloud Dataflow template pipelines for solving simple in-Cloud data tasks
lbergelson/DataflowTemplatesPy
Python dataflow templates for the BigQuery export project
lbergelson/disq
A library for manipulating bioinformatics sequencing formats in Apache Spark
lbergelson/docs-travis-ci-com
The Travis CI Documentation
lbergelson/Drop-seq
Java tools for analyzing Drop-seq data
lbergelson/fastai
The fastai deep learning library, plus lessons and tutorials
lbergelson/gatk-gui
Demonstration of a potential GATK GUI
lbergelson/GKL
Accelerated kernel library for genomics
lbergelson/gradle-signing-bug
Small reproduction of a gradle bug
lbergelson/homebrew-bio
:beer::microscope: Bioinformatics formulae for the Homebrew and Linuxbrew package managers
lbergelson/homebrew-core
🍻 Default formulae for the missing package manager for macOS
lbergelson/hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
lbergelson/htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
lbergelson/java-storage
lbergelson/java-storage-nio
lbergelson/jenv
Manage your Java environment
lbergelson/lunaris
lbergelson/parabricks-wdl
Accelerated genomics workflows in the Workflow Description Language
lbergelson/pipelines
Pipelines for processing malaria parasite and mosquito genome sequence data.
lbergelson/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.
lbergelson/revdepcheck
R package reverse dependency checking
lbergelson/Specifications
GFF and GVF specification documents
lbergelson/spotbugs
SpotBugs is FindBugs' successor. A tool for static analysis to look for bugs in Java code.
lbergelson/test-rename-branch
Testing how renaming a branch works
lbergelson/VarDictJava
VarDict Java port
lbergelson/zsh_whales_theme
My zsh theme