Repositories list

• melanoma-reanalysis

  Public
  Online Materials: Somatic Mutations, Neoepitope Homology and Inflammation in Melanomas Treated with CTLA-4 Blockade

  77 forks in hammerlab/melanoma-reanalysis•44 stars in hammerlab/melanoma-reanalysis•00 issues in hammerlab/melanoma-reanalysis•00 pull requests in hammerlab/melanoma-reanalysis•Updated Mar 22, 2026Mar 22, 2026

• guacamole

  Public
  Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly

  Scala

  •

  Apache License 2.0

  •2121 forks in hammerlab/guacamole•8585 stars in hammerlab/guacamole•4242 issues in hammerlab/guacamole•11 pull request in hammerlab/guacamole•Updated Mar 22, 2026Mar 22, 2026

• SmartCount

  Public
  Repository for collaboration on Celldom computer vision solutions

  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks in hammerlab/SmartCount•22 stars in hammerlab/SmartCount•1717 issues in hammerlab/SmartCount•11 pull request in hammerlab/SmartCount•Updated Aug 2, 2024Aug 2, 2024

• ppx_deriving_cmdliner

  Public
  Ppx_deriving plugin for generating command line interfaces from types (Cmdliner.Term.t)

  cliocamlppx+ 2

  cliocamlppxcommand-line-parserppx-extension

  OCaml

  •

  Apache License 2.0

  •1212 forks in hammerlab/ppx_deriving_cmdliner•9797 stars in hammerlab/ppx_deriving_cmdliner•1212 issues in hammerlab/ppx_deriving_cmdliner•11 pull request in hammerlab/ppx_deriving_cmdliner•Updated Sep 12, 2023Sep 12, 2023

• vcf-annotate-polyphen

  Public
  A tool to annotate human VCF files with PolyPhen2 effect measures

  Python

  •

  Apache License 2.0

  •66 forks in hammerlab/vcf-annotate-polyphen•1010 stars in hammerlab/vcf-annotate-polyphen•22 issues in hammerlab/vcf-annotate-polyphen•33 pull requests in hammerlab/vcf-annotate-polyphen•Updated Dec 26, 2022Dec 26, 2022

• flusso

  Public
  FCS (Flow Cytometry Standard) parser and utility

  JavaScript

  •

  Apache License 2.0

  •00 forks in hammerlab/flusso•22 stars in hammerlab/flusso•33 issues in hammerlab/flusso•77 pull requests in hammerlab/flusso•Updated Dec 9, 2022Dec 9, 2022

• t-cell-relation-extraction

  Public
  Literature mining for T cell relations

  Jupyter Notebook

  •55 forks in hammerlab/t-cell-relation-extraction•2323 stars in hammerlab/t-cell-relation-extraction•77 issues in hammerlab/t-cell-relation-extraction•55 pull requests in hammerlab/t-cell-relation-extraction•Updated Aug 5, 2022Aug 5, 2022

• cytokit

  Public
  Microscopy Image Cytometry Toolkit

  Jupyter Notebook

  •

  Apache License 2.0

  •1818 forks in hammerlab/cytokit•118118 stars in hammerlab/cytokit•1111 issues in hammerlab/cytokit•44 pull requests in hammerlab/cytokit•Updated Jul 15, 2022Jul 15, 2022

• flowdec

  Public
  TensorFlow Deconvolution for Microscopy Data

  Jupyter Notebook

  •

  Apache License 2.0

  •2424 forks in hammerlab/flowdec•9393 stars in hammerlab/flowdec•99 issues in hammerlab/flowdec•22 pull requests in hammerlab/flowdec•Updated Apr 29, 2022Apr 29, 2022

• genspio

  Public
  Generate Shell Phrases In OCaml

  shellocamledsl+ 2

  shellocamledslposixhacktoberfest

  OCaml

  •

  Apache License 2.0

  •33 forks in hammerlab/genspio•4747 stars in hammerlab/genspio•1616 issues in hammerlab/genspio•00 pull requests in hammerlab/genspio•Updated Dec 15, 2021Dec 15, 2021

• tcr-transfer

  Public
  Explore an alternative way to clone TILs by first single-cell TCR-seq'ing them and then transforming non-exhausted T cells with these TIL TCRs

  HTML

  •

  Apache License 2.0

  •00 forks in hammerlab/tcr-transfer•00 stars in hammerlab/tcr-transfer•66 issues in hammerlab/tcr-transfer•11 pull request in hammerlab/tcr-transfer•Updated Nov 30, 2021Nov 30, 2021

• biokepi

  Public
  Bioinformatics Ketrew Pipelines

  ocamlbioinformatics-pipelineketrew+ 1

  ocamlbioinformatics-pipelineketrewbioinformatics-ketrew-pipelines

  OCaml

  •

  Apache License 2.0

  •44 forks in hammerlab/biokepi•2727 stars in hammerlab/biokepi•8585 issues in hammerlab/biokepi•11 pull request in hammerlab/biokepi•Updated Nov 14, 2021Nov 14, 2021

• pileup.js

  Public
  Interactive in-browser track viewer

  JavaScript

  •

  Apache License 2.0

  •6262 forks in hammerlab/pileup.js•282282 stars in hammerlab/pileup.js•7979 issues in hammerlab/pileup.js•44 pull requests in hammerlab/pileup.js•Updated Oct 26, 2021Oct 26, 2021

• slim

  Public
  Node server that listens to Spark events, aggregates statistics, and writes them to Mongo

  JavaScript

  •

  Apache License 2.0

  •55 forks in hammerlab/slim•99 stars in hammerlab/slim•99 issues in hammerlab/slim•00 pull requests in hammerlab/slim•Updated Apr 6, 2021Apr 6, 2021

• spark-json-relay

  Public
  SparkListener that converts SparkListenerEvents to JSON and forwards them to an external service via RPC.

  Scala

  •

  Apache License 2.0

  •1111 forks in hammerlab/spark-json-relay•1616 stars in hammerlab/spark-json-relay•44 issues in hammerlab/spark-json-relay•00 pull requests in hammerlab/spark-json-relay•Updated Apr 6, 2021Apr 6, 2021

• spree

  Public
  Live-updating Spark UI built with Meteor

  JavaScript

  •

  Apache License 2.0

  •2929 forks in hammerlab/spree•189189 stars in hammerlab/spree•2222 issues in hammerlab/spree•11 pull request in hammerlab/spree•Updated Apr 6, 2021Apr 6, 2021

• sbt-parent

  Public
  SBT plugins for publishing to Maven Central, shading and managing dependencies, reporting to Coveralls from TravisCI, and more

  Scala

  •

  Apache License 2.0

  •33 forks in hammerlab/sbt-parent•1414 stars in hammerlab/sbt-parent•22 issues in hammerlab/sbt-parent•11 pull request in hammerlab/sbt-parent•Updated Nov 13, 2020Nov 13, 2020

• survivalstan

  Public
  Library of Stan Models for Survival Analysis

  Jupyter Notebook

  •

  Apache License 2.0

  •2222 forks in hammerlab/survivalstan•123123 stars in hammerlab/survivalstan•2222 issues in hammerlab/survivalstan•11 pull request in hammerlab/survivalstan•Updated Jul 15, 2020Jul 15, 2020

• spheroid

  Public
  Training data, models, and analysis for 3D culture cytotoxicity assays with microscopy

  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks in hammerlab/spheroid•00 stars in hammerlab/spheroid•00 issues in hammerlab/spheroid•00 pull requests in hammerlab/spheroid•Updated Nov 13, 2019Nov 13, 2019

• prohlatype

  Public
  Probabilistic HLA typing

  OCaml

  •

  Apache License 2.0

  •44 forks in hammerlab/prohlatype•3535 stars in hammerlab/prohlatype•1212 issues in hammerlab/prohlatype•00 pull requests in hammerlab/prohlatype•Updated Aug 31, 2019Aug 31, 2019

• awesome-clonality

  Public
  A curated list of awesome clonality and tumor heterogeneity resources

  Apache License 2.0

  •55 forks in hammerlab/awesome-clonality•1616 stars in hammerlab/awesome-clonality•11 issue in hammerlab/awesome-clonality•00 pull requests in hammerlab/awesome-clonality•Updated Jun 25, 2019Jun 25, 2019

• t-cell-activation

  Public
  Modeling bead based T cell activation to optimize ex vivo culturing conditions

  Jupyter Notebook

  •

  Apache License 2.0

  •11 fork in hammerlab/t-cell-activation•00 stars in hammerlab/t-cell-activation•00 issues in hammerlab/t-cell-activation•00 pull requests in hammerlab/t-cell-activation•Updated May 13, 2019May 13, 2019

• t-cell-electroporation

  Public
  Code/Data repository for "Electroporation characteristics of human primary T cells"

  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks in hammerlab/t-cell-electroporation•11 star in hammerlab/t-cell-electroporation•22 issues in hammerlab/t-cell-electroporation•00 pull requests in hammerlab/t-cell-electroporation•Updated Apr 20, 2019Apr 20, 2019

• dask-distributed-on-kubernetes

  Public
  Deploy dask-distributed on google container engine using kubernetes

  Jupyter Notebook

  •

  Apache License 2.0

  •55 forks in hammerlab/dask-distributed-on-kubernetes•4040 stars in hammerlab/dask-distributed-on-kubernetes•00 issues in hammerlab/dask-distributed-on-kubernetes•11 pull request in hammerlab/dask-distributed-on-kubernetes•Updated Apr 15, 2019Apr 15, 2019

• math-utils

  Public
  Math and statistics utilities

  Scala

  •

  Apache License 2.0

  •11 fork in hammerlab/math-utils•77 stars in hammerlab/math-utils•00 issues in hammerlab/math-utils•00 pull requests in hammerlab/math-utils•Updated Feb 11, 2019Feb 11, 2019

• pageant

  Public
  Parallel Genomic Analysis Toolkit

  44 forks in hammerlab/pageant•1414 stars in hammerlab/pageant•66 issues in hammerlab/pageant•00 pull requests in hammerlab/pageant•Updated Feb 11, 2019Feb 11, 2019

• flowrepository-metadata-db

  Public
  R

  •

  Apache License 2.0

  •00 forks in hammerlab/flowrepository-metadata-db•00 stars in hammerlab/flowrepository-metadata-db•00 issues in hammerlab/flowrepository-metadata-db•00 pull requests in hammerlab/flowrepository-metadata-db•Updated Jan 28, 2019Jan 28, 2019

• stancache

  Public
  Filecache for stan models

  reproducible-researchfilecachemcmc+ 1

  reproducible-researchfilecachemcmcstan-model

  Python

  •

  Apache License 2.0

  •11 fork in hammerlab/stancache•11 star in hammerlab/stancache•44 issues in hammerlab/stancache•00 pull requests in hammerlab/stancache•Updated Jan 16, 2019Jan 16, 2019

• magic-rdds

  Public
  Miscellaneous functionality for manipulating Apache Spark RDDs.

  Scala

  •44 forks in hammerlab/magic-rdds•2222 stars in hammerlab/magic-rdds•11 issue in hammerlab/magic-rdds•00 pull requests in hammerlab/magic-rdds•Updated Dec 29, 2018Dec 29, 2018

• spark-util

  Public
  low-level helpers for Apache Spark libraries and tests

  scalasparkhadoop+ 1

  scalasparkhadoopkryo

  Scala

  •

  Apache License 2.0

  •77 forks in hammerlab/spark-util•1616 stars in hammerlab/spark-util•11 issue in hammerlab/spark-util•00 pull requests in hammerlab/spark-util•Updated Dec 29, 2018Dec 29, 2018