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gatk
Official code repository for GATK versions 4 and upcromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environmentspicard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.keras-rcnn
Keras package for region-based convolutional neural networks (RCNNs)infercnv
Inferring CNV from Single-Cell RNA-Seqgtex-pipeline
GTEx & TOPMed data production and analysis pipelinespilon
Pilon is an automated genome assembly improvement and variant detection toolkeras-resnet
Keras package for deep residual networksCellBender
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.Tangram
Spatial alignment of single cell transcriptomic data.ssGSEA2.0
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)warp
WDL Analysis Research Pipelinesviral-ngs
Viral genomics analysis pipelinesseqr
web-based analysis tool for rare disease genomicsgatk-sv
A structural variation pipeline for short-read sequencingichorCNA
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.tensorqtl
Ultrafast GPU-enabled QTL mapperwot
A software package for analyzing snapshots of developmental processeslong-read-pipelines
Long read production pipelinesml4h
xtermcolor
Python library for terminal color support (including 256-color support)Drop-seq
Java tools for analyzing Drop-seq datadepmap_omics
What you need to process the Quarterly DepMap-Omics releases from Terramutect
MuTect -- Accurate and sensitive cancer mutation detectiongenomics-in-the-cloud
Source code and related materials for the O'Reilly bookgnomad_methods
Hail helper functions for the gnomAD project and Translational Genomics Grouppyro-cov
Pyro models of SARS-CoV-2 variantsgatk-docs
Documentation archive for GATK tools and workflowscatch
A package for designing compact and comprehensive capture probe sets.gnomad-browser
Explore gnomAD datasets on the weboncotator
gtex-viz
GTEx Visualizationssingle_cell_portal_core
Rails/Docker application for the Broad Institute's single cell RNA-seq data portalPhylogicNDT
docker-terraform
Docker container for running the Terraform applicationcromshell
CLI for interacting with Cromwell servers2020_scWorkshop
Code and data repository for the 2020 physalia course on single cell RNA sequencing.viral-pipelines
viral-ngs: complete pipelinesgnomad_qc
single_cell_portal
Tutorials, workflows, and convenience scripts for Single Cell Portalsam
workbench identity and access managementgistic2
Genomic Identification of Significant Targets in Cancer (GISTIC), version 2gamgee
A C++14 library for NGS data formatsdsde-deep-learning
DSDE Deep Learning Clubgtex-v8
Notebooks and scripts for reproducing analyses and figures from the V8 GTEx Consortium paperSignatureAnalyzer-GPU
GPU implementation of ARD NMFwdl-ide
Rich IDE support for Workflow Description LanguageCelligner_ms
Code related to the Celligner manuscriptcellpainting-gallery
Cell Painting Gallerycell-health
Predicting Cell Health with Morphological Profilesgatk-protected
Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk insteadpyqtl
Collection of analysis tools for quantitative trait locipython-cert_manager
Python interface to the Sectigo Certificate Manager REST APIStrainGE
strain-level analysis toolsfirecloud-orchestration
gdctools
Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons2019_scWorkshop
Repo for Physalia course Analysis of Single Cell RNA-Seq datafiss
FireCloud Service Selector (FISS) -- Python bindings and CLI for FireCloud execution enginesingle_cell_analysis
Documents used for workshops on single cell analysisdeepometry
Image classification for imaging flow cytometry.firepony
Efficient base quality score recalibrator for NGS dataadapt
A package for designing activity-informed nucleic acid diagnostics for viruses.pyfrost
Python bindings for Bifrost with a NetworkX compatible APIstr-analysis
Scripts and utilities related to analyzing short tandem repeats (STRs).rawls
Rawls service for DSDEprotigy
Proteomics Toolset for Integrative Data Analysisseqr-loading-pipelines
hail-based pipelines for annotating variant callsets and exporting them to elasticsearchlincs-cell-painting
Processed Cell Painting Data for the LINCS Drug Repurposing ProjectBipolarCell2016
cromwell-tools
A collection of Python clients and accessory scripts for interacting with the Cromwellsingle_cell_classification
Methods to use SNPs or gene expression to classify single cell RNAseq to reference profilesVariantBam
Filtering and profiling of next-generational sequencing data using region-specific ruleslongbow
Annotation and segmentation of MAS-seq datachronos
Modeling of time series data for CRISPR KO experimentsgtex-single-nucleus-reference
Code repository for the snRNA-seq cross-tissue atlas projectcovid19-testing
COVID-19 Diagnostic Processing DashboardAwesomeGenomics
Cancer Data Science's go to place for excellent genomics tools and packagesGATK-for-Microbes
firecloud-ui
FireCloud user interface for web browsers.BARD
BioAssay Research Databaseflipbook
A tool that lets you quickly flip through images in a local directory and record notes or answer questions about each one.palantir-workflows
Utility workflows for the DSP hydro.gen team (formerly palantir)wdltool
vim-wdl
Vim syntax highlighting for WDLwordpress-crowd-plugin
Crowd Authentication Plugin for Wordpressepi-SHARE-seq-pipeline
Epigenomics Program pipeline to analyze SHARE-seq data.mix_seq_ms
Code associated with MIX-seq manuscriptwiddler
A command-line tool for executing, managing, and querying WDL workflows on Cromwell servers.SpliceAI-lookup
Website for checking SpliceAI and Pangolin scores:imaging-platform-pipelines
Cell Painting and other pipelines from the Imaging Platformwdl-runner
Easily run WDL workflows on GCPcms
Composite of Multiple Signals: tests for selection in meiotically recombinant populationsscRNA-Seq
scalable_analytics
Public collaboration of Scalable Single Cell Analyticssparklespray
Easy batch submission of adhoc jobs onto GCPregional_missense_constraint
Code to calculate regional missense constraintdropviz
Shiny app for visualization, exploration of mouse brain single cell gene expressiongnomad_lof
hdf5-java-bindings
java bindings for hdf5Love Open Source and this site? Check out how you can help us