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pileup.js
Interactive in-browser track viewergrafana-spark-dashboards
Scripts for generating Grafana dashboards for monitoring Spark jobsspree
Live-updating Spark UI built with Meteorsurvivalstan
Library of Stan Models for Survival Analysiscytokit
Microscopy Image Cytometry Toolkitppx_deriving_cmdliner
Ppx_deriving plugin for generating command line interfaces from types (Cmdliner.Term.t)flowdec
TensorFlow Deconvolution for Microscopy Dataguacamole
Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assemblyketrew
Keep Track of Experimental Workflowsyarn-logs-helpers
Scripts for parsing / making sense of yarn logsgenspio
Generate Shell Phrases In OCamldask-distributed-on-kubernetes
Deploy dask-distributed on google container engine using kubernetesdata-canvas
Improved event handling and testing for the HTML5 canvascycledash
Variant Caller Analysis Dashboard and Data Management Systemprohlatype
Probabilistic HLA typingkubeface
python parallel map on kubernetesepidisco
Personalized cancer epitope discovery and peptide vaccine prediction pipelinesosa
The Sane OCaml String APIbiokepi
Bioinformatics Ketrew Pipelinesspark-tests
Utilities for writing tests that use Apache Spark.t-cell-relation-extraction
Literature mining for T cell relationsmulti-omic-urothelial-anti-pdl1
Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysisvcf.js
A VCF parser and variant record model in JavaScript.magic-rdds
Miscellaneous functionality for manipulating Apache Spark RDDs.cohorts
Utilities for analyzing mutations and neoepitopes in patient cohortsspark-bam
Load genomic BAM files using Apache Sparkpygdc
Python API for Genomic Data Commonsconcordance
Concordance between variant callersshapeless-utils
type-classes for structural manipulation of algebraic data typesbai-indexer
Build an index for your BAM Index (BAI)spark-json-relay
SparkListener that converts SparkListenerEvents to JSON and forwards them to an external service via RPC.coclobas
Configurable Cloudy Batch Schedulerspark-util
low-level helpers for Apache Spark libraries and testst-cell-guide
Human Primary T cells: A Practical Guideawesome-clonality
A curated list of awesome clonality and tumor heterogeneity resourcessbt-parent
SBT plugins for publishing to Maven Central, shading and managing dependencies, reporting to Coveralls from TravisCI, and moreimmuno
Use somatic mutations to choose a personalized cancer vaccine (tumor-specific immunogenic peptides)pageant
Parallel Genomic Analysis Toolkitseltest
The simple, fast, visual testing framework for web applications.stanity
python convenience functions for working with Stan models (via pystan)slim
Node server that listens to Spark events, aggregates statistics, and writes them to Mongovcf-annotate-polyphen
A tool to annotate human VCF files with PolyPhen2 effect measuresvaf-experiments
A step-by-step guide to estimate tumor clonality/purity from variant allele frequency datastyle-guides
Guidelines of the Hammer Labmath-utils
Math and statistics utilitieshlarp
Normalize HLA typing output.t-cell-data
iterators
Enrichment-methods for Scala collections (Iterators, Iterables, Arrays)infino
Infino: a Bayesian hierarchical model improves estimates of immune infiltration into tumor microenvironmentkerseq
Helpers for sequence prediction with Kerassecotrec
Setup Coclobas/Ketrew Clustersimmune-infiltrate-explorations
suffix-arrays
Spark-based implementation of pDC3, a linear-time parallel suffix-array-construction algorithmspark-genomics
Aggregation of various hammerlab-org genomic, spark, and scala librarieswobidisco
Workflows Bioinformatics and Discoballs: The Biokepiverseigv-httpfs
An adaptor which lets IGV talk to HDFS via HttpFSredaw
Reinvent the Dataset Wheelmelanoma-reanalysis
Online Materials: Somatic Mutations, Neoepitope Homology and Inflammation in Melanomas Treated with CTLA-4 Blockadeidiogrammatik
An extensible, embeddable karyogram for the browser.cli-utils
Helpers for creating command-line applicationstopeology
Compare neoepitope sequences with epitopes from IEDBstratotemplate
DEPRECATED: we don't really maintain this any more, we use Coclobas:ngsdiagnostics
Diagnostic Scripts for an NGS Pipelineogene
Type-safe scripts for genomic file wranglingbespoke.js
Parsers and fetchers for a cornucopia of bioinformatics formatsmhcflurry-icml-compbio-2016
Data and analysis notebooks for Predicting Peptide-MHC Binding Affinities With Imputed Training Datarinfino
R client to run infino (http://github.com/hammerlab/infino)coverage-depth
Generate genomic-coverage-depth histograms using Apache SparkSmartCount
Repository for collaboration on Celldom computer vision solutionsigvxml
Create IGV session files from the command-linepaper-aocs-chemo-neoantigens
Manuscript on chemotherapy-induced neoantigens in samples from the Australian Ovarian Cancer Studybdgenomics-notebook
flusso
FCS (Flow Cytometry Standard) parser and utilityio-utils
Libraries for console/file I/O, processing/formatting sizes in bytes, etc.variant-calling-benchmarks
Automated and curated variant calling benchmarks for Guacamolestratocumulus
DEPRECATED: we don't really maintain this any more, we use Coclobas:tcga-blca
Example analysis using Cohorts & TCGA-BLCA datacvutils
Computer vision utilitiespath-utils
Scala convenience-wrapper for java.nio.file.Pathdiscohorts
Generate Cohorts based on Epidisco and/or Biokepi resultsspear
WIP: SparkListener that maintains info about jobs, stages, tasks, executors, and RDDs in MongoDB.pysigs
Mutational signature deconvolution onto known signaturescelldom-analysis
Repository for Celldom experiment analysis and configurationt-cell-electroporation
Code/Data repository for "Electroporation characteristics of human primary T cells"genomic-loci
Utilities for representing genomic loci and reference-genomesstancache
Filecache for stan modelsgenomic-reads
Library for representing and working with genomic-sequencing reads.avm
Arteriovenous malformationsepidisco-web
Web interface to easily describe and submit epidisco jobsstring-utils
String/CSV utilitiesLove Open Source and this site? Check out how you can help us