Topic: "flow-cytometry"
whitews/FlowKit
A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces
Language: Python - Size: 137 MB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 172 - Forks: 51
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: 20 days ago - Pushed at: 20 days ago - Stars: 62 - Forks: 22
whitews/FlowIO
A Python library for reading and writing Flow Cytometry Standard (FCS) files
Language: Python - Size: 11.5 MB - Last synced at: 8 days ago - Pushed at: 24 days ago - Stars: 46 - Forks: 23
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: 8 months ago - Pushed at: over 8 years ago - Stars: 44 - Forks: 15
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: over 2 years ago - Stars: 39 - Forks: 23
burtonrj/CytoPy 📦
A data-centric flow/mass cytometry automated analysis framework
Language: Python - Size: 140 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 38 - Forks: 9
LCSB-BioCore/GigaSOM.jl
Huge-scale, high-performance flow cytometry clustering in Julia
Language: Julia - Size: 3.77 MB - Last synced at: 18 days ago - Pushed at: almost 2 years ago - Stars: 34 - Forks: 9
schienstockd/cecelia
Framework for image and flow cytometry analysis
Language: R - Size: 120 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 25 - Forks: 1
burkesquires/immunology-informatics 📦
Immunology Informatics - Big Data Analysis in Immunology - Tutorials
Language: R - Size: 278 MB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 21 - Forks: 6
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: 6.65 MB - Last synced at: about 6 hours ago - Pushed at: about 16 hours ago - Stars: 17 - Forks: 11
MorganConrad/fcs
Javascript / node.js code to read FCS flow cytometry data
Language: JavaScript - Size: 842 KB - Last synced at: 23 days ago - Pushed at: almost 2 years 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: 28 days ago - Pushed at: over 2 years ago - Stars: 16 - Forks: 7
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: 3 months ago - Pushed at: 4 months ago - Stars: 10 - Forks: 6
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: almost 2 years ago - Stars: 10 - Forks: 4
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: 4 months ago - Pushed at: 4 months ago - Stars: 9 - Forks: 8
buettnerlab/pytometry_legacy
This repository extends scanpy to handle flow and mass cytometry data.
Language: Jupyter Notebook - Size: 282 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 9 - Forks: 1
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
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: almost 4 years ago - Stars: 9 - 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: over 1 year ago - Pushed at: over 4 years ago - Stars: 8 - Forks: 5
laderast/flowDashboard
Shiny Modules for visualizing flow cytometry data
Language: R - Size: 10.7 MB - Last synced at: 24 days ago - Pushed at: almost 7 years ago - Stars: 8 - Forks: 2
maxsonBraunLab/CITEViz
CITEViz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq
Language: R - Size: 83.3 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 6 - Forks: 5
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: about 1 year ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 4
seaflow-uw/seaflowpy
Python package with library and CLI tool for analyzing SeaFlow data
Language: Python - Size: 31.8 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 5 - Forks: 3
plantarum/flowPloidy
An R package for flow cytometry histogram analysis
Language: R - Size: 6.41 MB - Last synced at: 4 days ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 0
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: almost 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 2
gitdemont/IFC
Tools for Imaging Flow Cytometry
Language: R - Size: 1.89 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 4 - Forks: 2
cellengine/fcs-validator
In-browser utility for validating FCS file specification compliance
Language: JavaScript - Size: 50.8 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0
whitews/ReFlow
Django-based Repository for Flow Cytometry Data
Language: JavaScript - Size: 8.62 MB - Last synced at: about 1 month ago - Pushed at: about 6 years ago - Stars: 4 - Forks: 1
gitdemont/IFCip
Image Processing tools for Imaging Flow Cytometry
Language: C++ - Size: 864 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - 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: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0
martindisch/fcs
Low-level Flow Cytometry Standard (FCS) file serializer/deserializer
Language: Rust - Size: 44.9 KB - Last synced at: 8 days ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 1
hylasD/tSpace
Language: R - Size: 91.5 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 1
DillonHammill/CytoGate
Plugin Gating Functions for openCyto
Language: R - Size: 121 MB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 3 - Forks: 0
xwu/FlowKit
A library for analyzing flow cytometry data
Language: Swift - Size: 371 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 0
gcampuzano14/LabCuro
Specialized clinical laboratory static file system manager.
Language: Python - Size: 107 MB - Last synced at: about 1 year ago - Pushed at: almost 8 years ago - Stars: 3 - Forks: 0
MartinPdeS/FlowCyPy
Python package for FlowCytometry simulation and development toolbox.
Language: Jupyter Notebook - Size: 179 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 2 - Forks: 0
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: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0
lance-waller-lab/gateR
Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Language: R - Size: 4.51 MB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 3
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: over 3 years ago - Stars: 2 - Forks: 3
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: 2 months ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0
seaflow-uw/fsc-size-calibration
Conversion from light scattering measured by SeaFlow to cell diameter
Language: R - Size: 19 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0
NathanSiemers/FauxFlow
FauxFlow - Analyze Single Cell Genomics Data in a Flow Cytometry Paradigm
Language: R - Size: 90.1 MB - Last synced at: 4 months ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0
mjendrusch/learning-ifc
Language: Python - Size: 11.4 MB - Last synced at: almost 2 years ago - Pushed at: almost 6 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: about 1 year ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 2
whitews/FlowVis
A collection of visualization examples for Flow Cytometry Data
Language: JavaScript - Size: 4.53 MB - Last synced at: 3 months ago - Pushed at: over 7 years ago - Stars: 2 - 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: about 1 year ago - Pushed at: almost 8 years ago - Stars: 2 - Forks: 2
plantarum/flowPloidy-old
This repo is deprecated. Use https://github.com/plantarum/flowPloidy instead!
Language: R - Size: 13.5 MB - Last synced at: almost 2 years ago - Pushed at: almost 8 years ago - Stars: 2 - Forks: 0
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: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0
arcadio/nk-models
CD56bright natural killer cells preferentially kill proliferating CD4+ T cells
Language: R - Size: 18.6 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 1
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
Kawameicha/indexSort
Retrieve index sorted data and visually explore .fcs data files.
Language: R - Size: 1.53 MB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 1 - 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: about 2 months ago - Pushed at: over 5 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: over 1 year ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 3
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: almost 2 years ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 0
miastay/gedit3
The Gene Expression Deconvolution Interactive Tool
Language: Svelte - Size: 147 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
alouchar/PhytoCytoTraits
Graphical User Interface to retrieve flow cytometry informations at the individual level.
Language: R - Size: 129 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
cellengine/cellengine-r-toolkit
CellEngine R API toolkit
Language: R - Size: 861 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
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: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - 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
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: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - 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: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
duke-hhis/reference-range
Interactive plots for the Grifols data set
Language: HTML - Size: 4.83 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
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: about 1 year ago - Pushed at: over 4 years ago - Stars: 0 - 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: almost 2 years 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: about 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
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: about 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: about 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1
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: about 1 year ago - Pushed at: over 5 years ago - Stars: 0 - 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: about 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: about 6 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: 8 days ago - Pushed at: almost 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: 8 days ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0
leipzig/fcs_upbrowse
CytoVas fcs uploader and file browser
Language: HTML - Size: 5.99 MB - Last synced at: 8 days ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0
SD2E/fcs-etl-application 📦
Flow cytometry ETL application.
Language: Python - Size: 145 KB - Last synced at: about 1 year 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: about 6 hours ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0
