Repositories list

• ggcyto

  Public
  Visualize Cytometry data with ggplot2

  HTML

  •

  MIT License

  •1818 forks•6565 stars•2525 issues•11 pull request•Updated Apr 18, 2026Apr 18, 2026

• flowCore

  Public
  Core flow cytometry infrastructure

  R

  •2525 forks•5757 stars•3838 issues•22 pull requests•Updated Apr 18, 2026Apr 18, 2026

• openCyto

  Public
  A package that provides data analysis pipeline for flow cytometry.

  R

  •

  GNU Affero General Public License v3.0

  •3232 forks•8383 stars•66 issues•1212 pull requests•Updated Mar 12, 2026Mar 12, 2026

• flowWorkspace

  Public
  flowWorkspace

  R

  •

  GNU Affero General Public License v3.0

  •2020 forks•4848 stars•5050 issues•22 pull requests•Updated Feb 19, 2026Feb 19, 2026

• CytoML

  Public
  A GatingML Interface for Cross Platform Cytometry Data Sharing

  HTML

  •

  GNU Affero General Public License v3.0

  •1515 forks•3535 stars•5656 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• MAST

  Public
  Tools and methods for analysis of single cell assay data in R

  R

  •5757 forks•262262 stars•3737 issues•11 pull request•Updated Oct 17, 2025Oct 17, 2025

• flowClust

  Public
  Bayesian flowClust

  R

  •88 forks•1111 stars•1010 issues•00 pull requests•Updated May 15, 2025May 15, 2025

• COMPASS

  Public
  Combinatorial Polyfunctionality Analysis of Single Cells

  R

  •1111 forks•88 stars•1616 issues•00 pull requests•Updated Feb 11, 2025Feb 11, 2025

• cytolib

  Public
  c++ library for representing and interacting the gated cytometry data structure

  C++

  •

  GNU Affero General Public License v3.0

  •1212 forks•1414 stars•99 issues•00 pull requests•Updated Jan 29, 2025Jan 29, 2025

• ncdfFlow

  Public
  A package that provides ncdf based storage for flow cytometry data.

  R

  •

  GNU Affero General Public License v3.0

  •77 forks•22 stars•33 issues•00 pull requests•Updated Jan 13, 2025Jan 13, 2025

• MIMOSA2

  Public
  Baseline Adjusted Positivity Calls for Intracellular Cytokine Staining Data

  R

  •22 forks•00 stars•00 issues•00 pull requests•Updated Aug 15, 2024Aug 15, 2024

• cytoUtils

  Public
  Helper tools for cytometry

  C++

  •11 fork•33 stars•22 issues•00 pull requests•Updated Dec 19, 2023Dec 19, 2023

• ImmuneSpaceR

  Public
  An R Interface to the ImmuneSpace database portal

  bioconductorimmunologylabkey+ 3

  bioconductorimmunologylabkeyimmunespaceimmporthipc

  R

  •1111 forks•2424 stars•00 issues•11 pull request•Updated Nov 28, 2023Nov 28, 2023

• FAUST

  Public
  Full annotation using shape-constrained trees

  C++

  •

  GNU General Public License v3.0

  •44 forks•3030 stars•44 issues•66 pull requests•Updated Sep 15, 2023Sep 15, 2023

• flowStats

  Public
  flowStats: algorithms for flow cytometry data analysis using BioConductor tools

  R

  •1010 forks•1414 stars•1818 issues•11 pull request•Updated Jul 19, 2023Jul 19, 2023

• RProtoBufLib

  Public
  bundled Protocol buffers library as an R package

  R

  •

  Other

  •33 forks•33 stars•66 issues•00 pull requests•Updated Jul 10, 2023Jul 10, 2023

• cytoqc

  Public
  A Quality Control tool for cytometry

  R

  •

  Other

  •33 forks•66 stars•55 issues•11 pull request•Updated Feb 8, 2023Feb 8, 2023

• LabKeyModules

  Public
  LabKey Modules for ImmuneSpace

  labkeyimmunespace

  labkeyimmunespace

  JavaScript

  •

  Artistic License 2.0

  •44 forks•55 stars•00 issues•00 pull requests•Updated Jan 25, 2023Jan 25, 2023

• UITesting

  Public
  ImmuneSpace UI Testing

  saucelabsrseleniumimmunespace

  saucelabsrseleniumimmunespace

  R

  •22 forks•22 stars•00 issues•00 pull requests•Updated Dec 14, 2022Dec 14, 2022

• HIPCMatrix

  Public
  Utilities for processing and analyzing HIPC gene expression data in ImmuneSpace

  rna-seqmicroarrayimmunespace+ 2

  rna-seqmicroarrayimmunespaceimmporthipc

  R

  •11 fork•11 star•00 issues•00 pull requests•Updated Dec 14, 2022Dec 14, 2022

• ImmuneSpaceCron

  Public
  Tools and functions for generating useful artifacts for ImmuneSpace Reports and APIs

  immunespace

  immunespace

  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Dec 14, 2022Dec 14, 2022

• ImmuneSpaceMaintenance

  Public
  Utility Package for ImmuneSpace Maintenance

  immunespace

  immunespace

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 13, 2022Dec 13, 2022

• AnalyteExplorer

  Public
  Analyte Explorer Pre-processing Scripts

  immunespacehipc

  immunespacehipc

  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 13, 2022Dec 13, 2022

• ImmuneSignatures

  Public
  HIPC ImmuneSignatures

  immunespaceimmunesignatureshipc

  immunespaceimmunesignatureshipc

  HTML

  •44 forks•11 star•22 issues•00 pull requests•Updated Dec 7, 2022Dec 7, 2022

• ImmuneSignatures2

  Public
  HIPC ImmuneSignatures2

  immunespaceimmunesignatureshipc

  immunespaceimmunesignatureshipc

  R

  •11 fork•11 star•00 issues•00 pull requests•Updated Dec 5, 2022Dec 5, 2022

• rcellontologymapping

  Public
  R interface to generate leukocyte cell classifications from cell surface markers using the decision tree from Maecker et al. (2012)

  Haskell

  •

  GNU Lesser General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 5, 2022Oct 5, 2022

• ImmPortR

  Public
  R wrapper around the ImmPort API and its download tool

  immport

  immport

  R

  •

  GNU General Public License v3.0

  •11 fork•33 stars•00 issues•00 pull requests•Updated Sep 1, 2022Sep 1, 2022

• flowViz

  Public
  Visualization for flow cytometry

  R

  •00 forks•1111 stars•33 issues•00 pull requests•Updated Aug 17, 2022Aug 17, 2022

• cytoverse.org

  Public
  HTML

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 18, 2022Mar 18, 2022

• covid19_sc

  Public
  Processing workflow for COVID-19 single cell data

  covid-19

  covid-19

  R

  •33 forks•1717 stars•44 issues•00 pull requests•Updated Dec 23, 2021Dec 23, 2021