GitHub topics: flow-cytometry
MartinPdeS/FlowCyPy
Python package for FlowCytometry simulation and development toolbox.
Language: Jupyter Notebook - Size: 320 MB - Last synced at: about 15 hours ago - Pushed at: about 17 hours ago - Stars: 5 - Forks: 0
lance-waller-lab/gateR
Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Language: R - Size: 4.8 MB - Last synced at: 4 days ago - Pushed at: 7 days ago - Stars: 2 - Forks: 3
AUMC-HEMA/MSGMM
The multi-sample Gaussian mixture model (MSGMM) is a clustering model adapted to fitting multiple samples simultaneously using the EM algorithm.
Language: R - Size: 16.6 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 0 - Forks: 0
LCSB-BioCore/GigaSOM.jl
Huge-scale, high-performance flow cytometry clustering in Julia
Language: Julia - Size: 3.95 MB - Last synced at: about 9 hours ago - Pushed at: 8 days ago - Stars: 35 - Forks: 9
whitews/FlowKit
A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces
Language: Python - Size: 137 MB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 184 - Forks: 53
martindisch/fcs
Low-level Flow Cytometry Standard (FCS) file serializer/deserializer
Language: Rust - Size: 44.9 KB - Last synced at: 4 days ago - Pushed at: about 3 years ago - Stars: 4 - Forks: 1
gitdemont/IFCip
Image Processing tools for Imaging Flow Cytometry
Language: C++ - Size: 664 KB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 3 - Forks: 0
clovestay/gedit3
The Gene Expression Deconvolution Interactive Tool
Language: Svelte - Size: 154 KB - Last synced at: 16 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
schienstockd/cecelia
Framework for image and flow cytometry analysis
Language: R - Size: 120 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 28 - Forks: 1
alouchar/Cyanobacteria-functional-ecology
The code aims at reproducing the analyses and figures presented in Louchart et al. (2025). Individual-level trait responses in natural cyanobacterial communities. The manuscript has been submitted to a journal.
Language: R - Size: 139 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
MavAayush/mrd-detection-flow
Unsupervised MRD detection in flow cytometry data using Variational AutoEncoder (VAE) and Gaussian Mixture Model (GMM).
Language: Jupyter Notebook - Size: 3.11 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
gabrielramirezv/CD43_in_erythropoiesis
In bone marrow, erythroblastic islands form around a central macrophage, where CD43 sialomucin on erythroblasts interacts with CD169 on macrophages, facilitating cell adhesion and supporting erythropoiesis. In this study, we evaluate the role of CD43 in erythroid differentiation.
Language: R - Size: 14.6 KB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
gitdemont/IFC
Tools for Imaging Flow Cytometry
Language: R - Size: 2.01 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 5 - Forks: 2
whitews/FlowUtils
FlowUtils is a Python package containing various utility functions related to flow cytometry analysis, primarily focused on compensation and transformation tasks commonly used within the flow community.
Language: Python - Size: 6.66 MB - Last synced at: 7 days ago - Pushed at: 3 months ago - Stars: 17 - Forks: 10
tlnagy/FCSFiles.jl
🧫 Read Flow Cytometry Standard (FCS) files in Julia
Language: Julia - Size: 3.45 MB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 17 - Forks: 7
whitews/FlowIO
A Python library for reading and writing Flow Cytometry Standard (FCS) files
Language: Python - Size: 11.5 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 46 - Forks: 23
ImmuneDynamics/Spectre
A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
Language: HTML - Size: 602 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 62 - Forks: 22
leonardlab/pyflowbat
An Open-Source Software Package for Performing High-Throughput Batch Analysis of Flow Cytometry Data
Language: Python - Size: 367 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 0
lmweber/cytometry-clustering-comparison
R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data
Language: R - Size: 3.68 MB - Last synced at: 2 months ago - Pushed at: over 8 years ago - Stars: 45 - Forks: 14
ucl-cssb/flopr
An R package for the processing of plate reader and flow cytometry data. This includes: normalisation and calibration of plate reader data, and removing debris and doublets and calibration of flow cytometry data.
Language: R - Size: 21.3 MB - Last synced at: 6 months ago - Pushed at: 7 months ago - Stars: 10 - Forks: 6
alouchar/PhytoCytoTraits
Graphical User Interface to retrieve flow cytometry informations at the individual level.
Language: R - Size: 129 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
seaflow-uw/seaflowpy
Python package with library and CLI tool for analyzing SeaFlow data
Language: Python - Size: 31.8 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 5 - Forks: 3
burtonrj/CytoPy 📦
A data-centric flow/mass cytometry automated analysis framework
Language: Python - Size: 140 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 38 - Forks: 9
seaflow-uw/popcycle
Popcycle is an R package that offers reproducible analytical tools to analyze flow cytometry data collected by SeaFlow
Language: R - Size: 49.4 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 9 - Forks: 8
cellengine/cellengine-r-toolkit
CellEngine R API toolkit
Language: R - Size: 861 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
arcadio/nk-models
CD56bright natural killer cells preferentially kill proliferating CD4+ T cells
Language: R - Size: 18.6 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1
plantarum/flowPloidy
An R package for flow cytometry histogram analysis
Language: R - Size: 6.41 MB - Last synced at: 4 days ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 0
maxsonBraunLab/CITEViz
CITEViz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq
Language: R - Size: 83.3 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 5
jrohel/CyFlowRec
CyFlowRec is software for collecting FCS (Flow Cytometry Standard) files received via the serial port (RS232 serial interface) from a Partec flow cytometer sent via the TRANSFER function.
Language: C - Size: 27.3 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
NUPulmonary/2020_Grant
Code base for the Grant, Morales-Nebreda, and Markov et al., “Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia” Nature (2021) paper
Language: Jupyter Notebook - Size: 42.4 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 6 - Forks: 4
burkesquires/immunology-informatics 📦
Immunology Informatics - Big Data Analysis in Immunology - Tutorials
Language: R - Size: 278 MB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 21 - Forks: 6
JimboMahoney/FCS-Events
Very fast method to read number of events from some / all FCS files in a directory
Language: R - Size: 2.93 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0
JimboMahoney/FlowCytSpeed
R Script to plot the average event rate in flow or mass cytometry (FCS) files
Language: R - Size: 109 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
JimboMahoney/FCS-Non-Redundancy-Score
Plots the NRS (non-redundancy score) of selected markers from one or more FCS files
Language: R - Size: 17.6 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1
JimboMahoney/FCS-Multidimensional-Scaling
Plots the MDS (Multi-dimensional scaling) of 3 or more FCS files.
Language: R - Size: 15.6 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
JimboMahoney/Common-FCS-Channels
Opens two or more FCS files and creates new files that contain only the Channels common to all.
Language: R - Size: 10.7 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
pathology-sandbox/flow_circos
Basic functionality to create circos plot that shows concurrent positivity of flow cytometry markers.
Language: R - Size: 6.38 MB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 2 - Forks: 2
gcampuzano14/LabCuro
Specialized clinical laboratory static file system manager.
Language: Python - Size: 107 MB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 3 - Forks: 0
wwu-mmll/gatenet
Official implementation of GateNet
Language: Jupyter Notebook - Size: 2.34 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
seaflow-uw/seaflow-virtualcore
Calibration of SeaFlow's Virtual Core
Language: R - Size: 1.02 GB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
harleyday/logicleTransform.m
MATLAB class to apply the logicle transformation to a matrix and provide axes labels.
Language: MATLAB - Size: 1.21 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
ParkerICI/premessa
R package for pre-processing of mass and flow cytometry data
Language: R - Size: 247 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 39 - Forks: 23
ParkerICI/panorama
R package for interactive visualization and analysis of single-cell data
Language: R - Size: 500 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 9 - Forks: 2
seaflow-uw/fsc-size-calibration
Conversion from light scattering measured by SeaFlow to cell diameter
Language: R - Size: 19 MB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 0
armbrustlab/cytDiv
cytoDiv is a R function that calculates ecological diversity indices for a microbial community based on its bio-optical properties measured at the single cell level by flow cytometry. The indices express the organization and structure of a community, its richness in physiological and genetic variations. The equations used to calculate the indices are described in Li, W. 1997 Limnology & Oceanography 42, 874:880
Language: R - Size: 1.13 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 2
rprops/Phenoflow_package
R package offering functionality for the advanced analysis of microbial flow cytometry data
Language: R - Size: 130 MB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 8 - Forks: 5
Team-Placenta-Golos-Lab/ZIKV-DAK-decidua-immune
Data processing for flow cytometry and LEGENDplex cytokine data described in "Decidual leukocytes respond to African lineage Zika virus infection with mild anti-inflammatory changes during acute infection in rhesus macaques
Language: R - Size: 284 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
cellengine/fcs-validator
In-browser utility for validating FCS file specification compliance
Language: JavaScript - Size: 50.8 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 4 - Forks: 0
gitdemont/IFCshiny
An R Interactive Shiny Application for the Analysis of Imaging and Conventional Flow Cytometry
Language: R - Size: 2.29 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0
plantarum/flowPloidy-old
This repo is deprecated. Use https://github.com/plantarum/flowPloidy instead!
Language: R - Size: 13.5 MB - Last synced at: about 2 years ago - Pushed at: about 8 years ago - Stars: 2 - Forks: 0
burkesquires/cytometry-clustering-comparison Fork of lmweber/cytometry-clustering-comparison
R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data
Language: R - Size: 3.68 MB - Last synced at: about 2 years ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 0
k-palffy/cytobins
An R package for simple, customizable binning of flow cytometric data
Language: R - Size: 4.29 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
MorganConrad/fcs
Javascript / node.js code to read FCS flow cytometry data
Language: JavaScript - Size: 842 KB - Last synced at: 19 days ago - Pushed at: about 2 years ago - Stars: 17 - Forks: 10
seaflow-uw/fsc-poc-calibration
Conversion from light scattering measured by SeaFlow to carbon per cell
Language: R - Size: 21.7 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0
ParkerICI/vite
R package for analysis of single-cell data using graphs
Language: R - Size: 128 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 10 - Forks: 4
ParkerICI/grappolo
R package to cluster single-cell data and generate features that can be used for model building
Language: R - Size: 82 KB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 9 - Forks: 2
CMET-UGent/Phenoflow_package Fork of rprops/Phenoflow_package
R package offering functionality for the advanced analysis of microbial flow cytometry data
Language: HTML - Size: 130 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 2
laderast/flowDashboard
Shiny Modules for visualizing flow cytometry data
Language: R - Size: 10.7 MB - Last synced at: 4 months ago - Pushed at: about 7 years ago - Stars: 8 - Forks: 2
SD2E/fcs-etl-application 📦
Flow cytometry ETL application.
Language: Python - Size: 145 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0
fribalet/ssPopModel
Size-structured matrix population model for SeaFlow data
Language: Jupyter Notebook - Size: 44.4 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 3
buettnerlab/pytometry_legacy
This repository extends scanpy to handle flow and mass cytometry data.
Language: Jupyter Notebook - Size: 282 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 9 - Forks: 1
whitews/ReFlow
Django-based Repository for Flow Cytometry Data
Language: JavaScript - Size: 8.62 MB - Last synced at: 4 months ago - Pushed at: over 6 years ago - Stars: 4 - Forks: 1
whitews/FlowVis
A collection of visualization examples for Flow Cytometry Data
Language: JavaScript - Size: 4.53 MB - Last synced at: 6 months ago - Pushed at: almost 8 years ago - Stars: 2 - Forks: 0
morchalabi/COMPARE-suite
Novel ultrafast suite for high-throughput & high-content multiparameter screening as in drug discovery. It has unique modules for QC, bias correction, similarity measurement, clustering and visualization. It can process hundreds of samples with many markers in a few hours not days & circumvents bath effect. It couples with any plate reader.
Language: R - Size: 32.6 MB - Last synced at: 6 months ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0
mjendrusch/learning-ifc
Language: Python - Size: 11.4 MB - Last synced at: about 1 month ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 0
hylasD/tSpace
Language: R - Size: 91.5 MB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 3 - Forks: 1
duke-hhis/reference-range
Interactive plots for the Grifols data set
Language: HTML - Size: 4.83 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
Kawameicha/indexSort
Retrieve index sorted data and visually explore .fcs data files.
Language: R - Size: 1.53 MB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0
sriramsrikant/2020-CB_ABC-selectivity
Code-base for my ABC-selectivity paper in Current Biology
Language: Jupyter Notebook - Size: 2.52 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
NathanSiemers/FauxFlow
FauxFlow - Analyze Single Cell Genomics Data in a Flow Cytometry Paradigm
Language: R - Size: 90.1 MB - Last synced at: 7 months ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0
SilasBoyeNissen/Silicates-Eroded-under-Simulated-Martian-Conditions-Effectively-Kill-Bacteria
"Silicates Eroded under Simulated Martian Conditions Effectively Kill Bacteria - A Challenge for Life on Mars" published in Frontiers in Microbiology (2017)
Size: 33.9 MB - Last synced at: 5 months ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0
prubbens/InSilicoFlow
Repository accompanying the paper "Flow cytometric single-cell identification of populations in synthetic bacterial communities".
Language: Python - Size: 171 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 3
xwu/FlowKit
A library for analyzing flow cytometry data
Language: Swift - Size: 371 KB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 0
gaberosenfield/Glass-Lab-Flow-Cytometry-Analysis
Contains MATLAB scripts used by members of the Glass Lab at UC Berkeley to analyze flow cytometry data.
Language: MATLAB - Size: 4.37 MB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
hylasD/MATLAB_version_tSpace
Language: MATLAB - Size: 532 KB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
DillonHammill/CytoGate
Plugin Gating Functions for openCyto
Language: R - Size: 121 MB - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 3 - Forks: 0
leipzig/fcs_upbrowse
CytoVas fcs uploader and file browser
Language: HTML - Size: 5.99 MB - Last synced at: 4 days ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0
leipzig/fcs_batch_titration
batch-titration is a container that allows for one or more fcs files to be automatically processed (using AWS Batch or other runners). It produces an html document.
Language: R - Size: 1.44 MB - Last synced at: 4 days ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0
leipzig/fcs_lambda
parse fcs files in s3 and store various metadata in dynamodb
Language: Python - Size: 218 KB - Last synced at: 4 days ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0
vaulot/R_flow-cytometry-correction
Correction for flow cytometry histograms when part of the population is in noise
Language: R - Size: 7.81 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0
j4c0bs/xfcs
FCS (3.0, 3.1) data and metadata extractor
Language: Python - Size: 234 KB - Last synced at: 18 days ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0
