Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: cytometry
ghar1821/Chronoclust
A clustering algorithm that will perform clustering on each of a time-series of discrete datasets, and explicitly track the evolution of clusters over time.
Language: Python - Size: 44.1 MB - Last synced: 1 day ago - Pushed: over 3 years ago - Stars: 15 - Forks: 3
PaulRegnier/PICAFlow
PICAFlow: a complete R workflow dedicated to flow/mass cytometry data, from data pre-processing to deep and comprehensive analysis.
Language: R - Size: 334 KB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 1 - Forks: 0
tidyomics/tidyomics
Easily install and load packages from the tidyomcis ecosystem
Language: R - Size: 107 KB - Last synced: 2 days ago - Pushed: 3 months ago - Stars: 20 - Forks: 0
whitews/FlowKit
A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces
Language: Python - Size: 148 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 148 - Forks: 33
MICS-Lab/scyan
Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effect and can be used for debarcoding or population discovery.
Language: Python - Size: 25.7 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 30 - Forks: 1
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: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0
Lindell-Lab/MODS-Subphenotypes
Repository for MODS subphenotype preprint, data, and code.
Size: 12.8 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0
BodenmillerGroup/histocat-web
Histology Topography Cytometry Analysis Toolbox (histoCAT) for Web.
Language: Vue - Size: 31.6 MB - Last synced: 18 days ago - Pushed: 11 months ago - Stars: 8 - Forks: 9
gszep/FlowAtlas.jl
an interactive explorer for flow cytometry data
Language: JavaScript - Size: 1.06 GB - Last synced: 25 days ago - Pushed: 7 months ago - Stars: 9 - Forks: 0
nf-core/imcyto
Image Mass Cytometry analysis pipeline
Language: Python - Size: 8.77 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 23 - Forks: 15
keyes-timothy/tidytof
An R package for analyzing high-dimensional cytometry data using the tidyverse.
Language: R - Size: 603 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 16 - Forks: 4
YogiOnBioinformatics/B-Cells-In-Atherosclerosis
Work done during rotation with Coleen McNamara & Stefan Bekiranov in UVA BIMS PhD program
Language: Jupyter Notebook - Size: 1.5 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
scivision/cytometry-ratios 📦
Open source static cytometry, initially targeting P. falciparum malaria
Language: Python - Size: 13.8 MB - Last synced: about 1 month ago - Pushed: almost 4 years ago - Stars: 2 - Forks: 0
whitews/FlowIO
A Python library for reading and writing Flow Cytometry Standard (FCS) files
Language: Python - Size: 5 MB - Last synced: 21 days ago - Pushed: 2 months ago - Stars: 38 - Forks: 16
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: 1010 KB - Last synced: 21 days ago - Pushed: 2 months ago - Stars: 13 - Forks: 8
gitdemont/IFC
Tools for Imaging Flow Cytometry
Language: R - Size: 2.25 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 4 - Forks: 2
LCSB-BioCore/GigaSOM.jl
Huge-scale, high-performance flow cytometry clustering in Julia
Language: Julia - Size: 3.77 MB - Last synced: 25 days ago - Pushed: 11 months ago - Stars: 29 - Forks: 9
JimboMahoney/CytobankGraphs
R Script for reading CyTOF or flow cytometry data (FCS) and generating plots like Cytobank
Language: R - Size: 1.36 MB - Last synced: 3 months ago - Pushed: over 4 years ago - Stars: 2 - Forks: 1
JimboMahoney/CyTOF-PlotViewer
Plots log histograms of FCS files like CyTOF's PlotViewer program
Language: R - Size: 298 KB - Last synced: 3 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 1
phipsonlab/SuperCellCyto
SuperCell for Cytometry data
Language: R - Size: 64.6 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 5 - Forks: 0
gitdemont/IFCip
Image Processing tools for Imaging Flow Cytometry
Language: C++ - Size: 864 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 3 - Forks: 0
CIDARLAB/fpSelection
Algorithms for the selection of fluorescent reporters.
Language: Java - Size: 101 MB - Last synced: 4 months ago - Pushed: about 2 years ago - Stars: 5 - Forks: 3
lance-waller-lab/gateR
Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Language: R - Size: 4.51 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 2
wwu-mmll/gatenet
Official implementation of GateNet
Language: Jupyter Notebook - Size: 2.34 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
MapleBKL/cytometry-autogating
Autogating for gate 1 and gate 2 with U-Net.
Language: Python - Size: 2.92 MB - Last synced: 5 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
JimboMahoney/CytoBars
R script for summarising paramater / channel intensity from flow or mass cytometry data
Language: R - Size: 81.1 KB - Last synced: 3 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0
ghar1821/TrackSOM
Temporal clustering and tracking algorithm which fuses on FlowSOM and ChronoClust, specifically designed for analysing temporal cytometry data
Language: R - Size: 11.2 MB - Last synced: 22 days ago - Pushed: 6 months ago - Stars: 6 - Forks: 1
TAPE-Lab/CyGNAL
Pipeline for analysing and visualising CyTOF datasets, with a focus on PTM signalling networks.
Language: Python - Size: 50.1 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 6 - Forks: 7
LogIN-/fluprint
Import script needed to build FluPRINT database from source :computer:
Language: PHP - Size: 96.7 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 11 - Forks: 3
casanova-lab/iMUBAC
Integration of multi-batch cytometry datasets
Language: R - Size: 11.1 MB - Last synced: 8 months ago - Pushed: over 1 year ago - Stars: 8 - Forks: 7
mingchen-lab/cytosee
online version please visit
Language: R - Size: 576 KB - Last synced: 8 months ago - Pushed: about 5 years ago - Stars: 1 - Forks: 1
luglilab/Cytophenograph
Pipeline for flow cytometry anlaysis
Language: Python - Size: 363 MB - Last synced: 9 months ago - Pushed: 10 months ago - Stars: 2 - 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: 9 months ago - Pushed: 9 months ago - Stars: 3 - Forks: 0
burtonrj/CytoPy
A data-centric flow/mass cytometry automated analysis framework
Language: Python - Size: 143 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 34 - Forks: 11
exaexa/EmbedSOM
Fast embedding ot multidimensional datasets, great for cytometry data
Language: R - Size: 189 KB - Last synced: 13 days ago - Pushed: almost 2 years ago - Stars: 24 - Forks: 5
i-cyto/cytoBatchNorm_archive
A R package to apply Batch Normalization to cytometry
Language: R - Size: 4.52 MB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 1 - 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: 10 months ago - Pushed: over 7 years ago - Stars: 1 - Forks: 0
Terkild/CITE-seq_optimization
Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
Language: R - Size: 210 MB - Last synced: 8 months ago - Pushed: about 3 years ago - Stars: 9 - Forks: 2
matei-ionita/HiTMapper
An R package for visualization and relational analysis of cell states, based on the Mapper algorithm from topological data analysis.
Language: C++ - Size: 7.81 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 3 - Forks: 2
i-cyto/cytoBatchNorm
A R package to apply Batch Normalization to cytometry
Language: R - Size: 4.46 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 2 - Forks: 0
SangerCytometry/R-Scripts 📦
R scripts to help with your flow cytometry analysis. Batch index export and overlays
Language: R - Size: 2.4 MB - Last synced: over 1 year ago - Pushed: over 4 years ago - Stars: 1 - Forks: 2
SangerCytometry/Influx-index-file-counter 📦
Counts index files and folders produced by the BD Influx
Language: Python - Size: 4.81 MB - Last synced: over 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0
SangerCytometry/Influx-workspace-renamer 📦
Rename your BD Influx workspaces to the same name found in the 'Name' tag of the workspace
Language: Python - Size: 4.89 MB - Last synced: over 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0
SangerCytometry/XDP-sort-statistics 📦
Extracts the sort statistics from the XDP server
Language: Python - Size: 7.95 MB - Last synced: over 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0
ZELLMECHANIK-DRESDEN/ShapeOut 📦
Shape-Out has been superseded by Shape-Out 2.
Language: Python - Size: 5.55 MB - Last synced: 25 days ago - Pushed: almost 4 years ago - Stars: 5 - Forks: 5
niaid/HDStIM
HDStIM: High Dimensional Stimulation Immune Mapping
Language: R - Size: 42.3 MB - Last synced: 7 months ago - Pushed: 8 months ago - Stars: 3 - Forks: 0
rohitfarmer/ColabHDStIM
Google Colab interface to HDStIM (High Dimensional Stimulation Immune Mapping)
Language: Jupyter Notebook - Size: 628 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
mastroalex/ecm-mmt
The equivalent circuit model for a parallel electrode impedance cytometer is analyzed together with Maxwell's theory of homogenization of mixtures. It deals with both a modeling single and double shell.
Language: MATLAB - Size: 2.58 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
bmiles/flowcytometry
Transcriptic package for flow cytometry to demonstrate continuous integration for experiments
Language: Python - Size: 57.6 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0
RGLab/HIPCCyto
HIPC Cytometry
Language: R - Size: 308 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0
BodenmillerGroup/bbsnippets
This repository contains general examples, code snippets and guidelines.
Language: HTML - Size: 57.1 MB - Last synced: 18 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1
klavinslab/cowfish
Cowfish: an Aquarium cytometry results analyzing package in Python
Language: Python - Size: 43 KB - Last synced: 2 months ago - Pushed: about 5 years ago - Stars: 2 - Forks: 1
DillonHammill/CytoExploreR-Map
Comparison of Dimensionality Reduction Techniques in CytoExploreR
Size: 7.81 KB - Last synced: over 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0
tim-tx/microscopy-pipeline
A meta-package to test pipelines of image processing tools and cytometry-style calibration.
Language: Python - Size: 23.4 KB - Last synced: over 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0
