cytometry

There are 0 repository under cytometry topic.

whitews / FlowKit
A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces
cytometry data-science fcs fcs-files flow-cytometry flow-cytometry-analysis flowjo gatingml immunology python
Language:Python 169
tidyomics / tidyomics
Easily install and load packages from the tidyomcis ecosystem
cytometry genomics tidyverse transcriptomics
Language:R 65
whitews / FlowIO
A Python library for reading and writing Flow Cytometry Standard (FCS) files
python fcs flow-cytometry flow-cytometry-analysis flow-cytometry-files fcs-files cytometry immunology
Language:Python 45
burtonrj / CytoPy
A data-centric flow/mass cytometry automated analysis framework
cytometry-analysis-pipeline cytometry-data cytometry python mongodb document-database flow-cytometry flow-cytometry-analysis mass-cytometry immunology immunophenotyping machine-learning clustering framework
Language:Python 39
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.
cytometry deep-learning generative-model normalizing-flows single-cell-omics
Language:Python 34
LCSB-BioCore / GigaSOM.jl
Huge-scale, high-performance flow cytometry clustering in Julia
artifical-neural-network artificial-intelligence clustering clustering-methods cytof cytometry flow-cytometry huge-scale immunology large-scale mass-cytometry neural-networks self-organizing-map som
Language:Julia 32
exaexa / EmbedSOM
Fast embedding ot multidimensional datasets, great for cytometry data
cytometry rstats som visualization
Language:R 26
nf-core / imcyto
Image Mass Cytometry analysis pipeline
nf-core nextflow workflow image-analysis image-processing image-segmentation cytometry pipeline
Language:Python 25
keyes-timothy / tidytof
An R package for analyzing high-dimensional cytometry data using the tidyverse.
bioinformatics cytometry data-science r rstats single-cell tidyverse
Language:R 18
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.
bioinformatics cluster-tracking clustering cytometry time-series-clustering
Language:Python 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.
python fcs flow-cytometry fcs-files flow flow-cytometry-analysis flow-cytometry-data cytometry
Language:Python 15
gszep / FlowAtlas.jl
an interactive explorer for flow cytometry data
cytometry single-cell flowjo dimensionality-reduction clustering annotation interactive-visualizations julia
Language:JavaScript 12
phipsonlab / SuperCellCyto
SuperCell for Cytometry data
bioinformatics computational-biology cytometry r
Language:R 12
LogIN- / fluprint
Import script needed to build FluPRINT database from source :computer:
cytometry dataset dataset-generation immune-system influenza molecular-underpinnings phospho-flow vaccine
Language:PHP 11
Terkild / CITE-seq_optimization
Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
antibody cite-seq cytometry single-cell-omics single-cell-proteomics single-cell-rna-seq
Language:R 9
casanova-lab / iMUBAC
Integration of multi-batch cytometry datasets
cytof cytometry flowsom immunophenotyping machine-learning r
Language:R 8
ghar1821 / TrackSOM
Temporal clustering and tracking algorithm which fuses on FlowSOM and ChronoClust, specifically designed for analysing temporal cytometry data
bioinformatics clustering cytometry time-series-analysis
Language:R 8
wwu-mmll / gatenet
Official implementation of GateNet
cytof cytometry flow-cytometry gating mass-cytometry single-cell
Language:Jupyter Notebook 8
BodenmillerGroup / histocat-web
Histology Topography Cytometry Analysis Toolbox (histoCAT) for Web.
imc vue python fastapi cytometry single-cell data-visualization segmentation scientific toolbox bioinformatics
Language:Vue 7
TAPE-Lab / CyGNAL
Pipeline for analysing and visualising CyTOF datasets, with a focus on PTM signalling networks.
cytof cell-communication-lab cytobank data-analysis scprep emd dremi pca umap tape-lab organoids signalling ptm ptms mass cytometry fcs visualization visualisation
Language:Python 7
CIDARLAB / fpSelection
Algorithms for the selection of fluorescent reporters.
cytometry fluorescence scientific-computing scientific-workflows selection-algorithms webapp workflow
Language:Java 6
luglilab / Cytophenograph
Pipeline for flow cytometry anlaysis
phenograph cytometry-analysis-pipeline singlecell python3 cytometry flowsom parc flowcytometry
Language:Python 6
saeyslab / ViScore
Single-cell dimensionality reduction evaluation and benchmarking toolkit
benchmarking cytometry dimensionality-reduction scrna-seq single-cell-analysis
Language:Python 6
gitdemont / IFCshiny
An R Interactive Shiny Application for the Analysis of Imaging and Conventional Flow Cytometry
r ifc flow-cytometry flow-cytometry-analysis flow-cytometry-data flow-cytometry-files cytometry cytometry-data imaging-flow-cytometry imaging-flow-cytometry-data image-processing flow image microscopy
Language:R 5
ZELLMECHANIK-DRESDEN / ShapeOut
Shape-Out has been superseded by Shape-Out 2.
cytometry cell-analysis cell-mechanics high-throughput
Language:Python 5
gitdemont / IFC
Tools for Imaging Flow Cytometry
ifc flow cytometry image cytometry-data flow-cytometry imaging-flow-cytometry flow-cytometry-data imaging-flow-cytometry-data microscopy r flow-cytometry-analysis flow-cytometry-files
Language:R 4
matei-ionita / HiTMapper
An R package for visualization and relational analysis of cell states, based on the Mapper algorithm from topological data analysis.
visualization graph cytometry clustering
Language:C++ 4
gitdemont / IFCip
Image Processing tools for Imaging Flow Cytometry
flow image r image-processing ifc microscopy flow-cytometry flow-cytometry-analysis flow-cytometry-data flow-cytometry-files cytometry imaging-flow-cytometry imaging-flow-cytometry-data cytometry-data
Language:C++ 3
i-cyto / cytoBatchNorm
An R package to apply Batch Normalization to cytometry
cytometry r-package
Language:R 3
niaid / HDStIM
HDStIM: High Dimensional Stimulation Immune Mapping
cytometry cytometry-analysis-pipeline cytof flowcytometry stimulation assay r-package
Language:R 3
saeyslab / ViVAE
Single-cell dimensionality reduction toolkit
cytometry deep-learning differential-geometry dimensionality-reduction mds scrna-seq single-cell-analysis
Language:Jupyter Notebook 3
gitdemont / IFCdata
Data for Imaging Flow Cytometry
ifc flow cytometry image cytometry-data flow-cytometry imaging-flow-cytometry imaging-flow-cytometry-data microscopy flow-cytometry-data flow-cytometry-files r
Language:R 2
lance-waller-lab / gateR
Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
cran cran-r cytometry flow-cytometry gating kernel-density-estimation mass-cytometry non-euclidean-spaces r r-package rstats rstats-package spatial-analysis
Language:R 2
PaulRegnier / PICAFlow
PICAFlow: a complete R workflow dedicated to flow/mass cytometry data, from data pre-processing to deep and comprehensive analysis.
cluster cluster-analysis clustering clustering-algorithm cytometry cytometry-analysis-pipeline cytometry-data downsampling fcs fcs-files immunological-bioinformatics immunological-data immunology normalization transformation
Language:R 2
pritampanda15 / Proteomics
Flow Cytometry analysis in R | Proteomics
cytoexplorer cytometry cytometry-analysis-pipeline flow flowcytometry
Language:HTML 2
scivision / cytometry-ratios
Open source static cytometry, initially targeting P. falciparum malaria
cytometry malaria
Language:Python 2