cinquin

attaching_jshell

Attach Java 9's JShell to already-running virtual machine

MEME

MEME motif-based sequence analysis tools (http://meme-suite.org), with FreeBSD tweaks

ChIP-GPT-llm

Code to train and run Llama-based model to extract data from SRA records

parismi

Pipeline for 3D segmentation and analysis of biological sample images

mutinack

Mutation detection program

akuma

Embeddable daemonization library

bam-readcount

count DNA sequence reads in BAM files

GNU_Trove

Fork of GNU Trove Bitbucket repository, with extra methods to be used with lambdas

javac_bug

pitest

State of the art mutation testing system for the JVM

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences; edited to compile under FreeBSD

eclipse-collections

The Eclipse Collections Project

error-prone

Catch common Java mistakes as compile-time errors

fast-serialization

FST: fast java serialization drop in-replacement http://ruedigermoeller.github.io/fast-serialization/

final_annotation

gleason_CNN

guava

Google Core Libraries for Java

honest-profiler

A sampling JVM profiler without the safepoint sample bias

htslib

C library for high-throughput sequencing data formats

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

jmh

Git import of http://hg.openjdk.java.net/code-tools/jmh, with modifications to add Generated annotations

jq

Command-line JSON processor

LASER

LASER: Locating Ancestry from SEquence Reads

nailgun

Nailgun is a client, protocol, and server for running Java programs from the command line without incurring the JVM startup overhead.

openssl

OpenSSL bindings for R

pathvisio

PathVisio

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

rmiio

Mirror of the RMIIO project: http://openhms.sourceforge.net/rmiio/

StoCySim

XChart

XChart is a light weight Java library for plotting data.