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bazam

A read extraction and realignment tool for next generation sequencing data

beakerx

Beaker Extensions for Jupyter Notebook

beakerx_kernel_autotranslation

A repository for BeakerX Autotranslation components.

beakerx_kernel_base

Base repository for BeakerX JVM based kernels

beakerx_kernel_groovy

beakerx_tabledisplay

beakerx_tests

bioinformatics-workflows

minimal example implementations for bioinformatics workflow managers

bpipe

Bpipe - a tool for running and managing bioinformatics pipelines

cn.mops

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/cn.mops.html Contributions: http://www.bioinf.jku.at/software/cnmops/cnmops.html. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=cn.mops.

cpipe

The open source version of the Melbourne Genomics Health Alliance Exome Sequencing Pipeline

derbydebug

Demonstration of a failure with Apache Derby

excelcatgory

A small utility to ease making Excel files with groovy

exome_depth_pipeline

A Bpipe pipeline for easily running ExomeDepth

gatk

GATK Official Release Repository

gatks

A scripting interface to the Genome Analysis Toolkit (GATK)

graxxia

Wrappers for doing Mathematics in Groovy

groovy-hts-sample-info

groovy-ngs-utils

A collection of utilities for working with next generation (MPS) sequencing data in Groovy

groovy-stream

A collection of classes to give a fluent builder for Streams (Lazy Groovy Generators)

hail-elasticsearch-pipelines

hail-based pipelines for annotating variant callsets and exporting them to elasticsearch

halo_dsd

The pipeline and read trimming code used for analysing HaloPlex data at MCRI

htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

igv

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

intervaltree

A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment.

jahmm

A Java Hidden Markov Model library

jessies

Terminator, Evergreen, lwm and friends

jsoncodegen

Groovy based generation tasks from JSON schema

koada

Front end for llama2-code-instruct

kubernetes-elasticsearch-cluster

Elasticsearch cluster on top of Kubernetes made easy.