mass-cytometry
There are 3 repositories under mass-cytometry topic.
ImmuneDynamics / Spectre
A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
Language:HTML 57lmweber / cytometry-clustering-comparison
R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data
Language:R 44- Language:R 42
- Language:Python 38
LCSB-BioCore / GigaSOM.jl
Huge-scale, high-performance flow cytometry clustering in Julia
Language:Julia 31- Language:R 11
- Language:R 10
buettnerlab / pytometry_legacy
This repository extends scanpy to handle flow and mass cytometry data.
Language:Jupyter Notebook 9ParkerICI / grappolo
R package to cluster single-cell data and generate features that can be used for model building
Language:R 9- Language:Jupyter Notebook 7
MarioniLab / archive-cydar
An archived version of the cydar repository, see https://github.com/MarioniLab/cydar for the active version.
Language:R 6- Language:Python 3
JimboMahoney / cytofclean
Fast auto-cleanup of CyTOF data
Language:R 3deMirandaLab / PENGUIN
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
Language:Jupyter Notebook 2R Script for reading CyTOF or flow cytometry data (FCS) and generating plots like Cytobank
Language:R 2lance-waller-lab / gateR
Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Language:R 2morchalabi / 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 2burkesquires / cytometry-clustering-comparison
R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data
Language:R 1dweth / mcsnac
Code for analysis of single cell signaling network kinetics from flow cytometry (CyTOF) datasets
Language:Fortran 1R script for summarising paramater / channel intensity from flow or mass cytometry data
Language:R 1Plots log histograms of FCS files like CyTOF's PlotViewer program
Language:R 1Code and manuscript files for Aaron and Arianne's differential abundance methodology manuscript.
Language:TeX 1jeffreypullin / myCyTOF
Functions and scripts for analysing and normalising CyTOF data
Language:HTML 0Opens two or more FCS files and creates new files that contain only the Channels common to all.
Language:R 0Plots the MDS (Multi-dimensional scaling) of 3 or more FCS files.
Language:R 0Plots the NRS (non-redundancy score) of selected markers from one or more FCS files
Language:R 0marta-seq / PENGUIN
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
Language:Jupyter Notebook 0SimeonGeorgiev / msc_project
Batch effect correction and automated gating of CyTOF data
Language:Jupyter Notebook 0Teng-Qiu-Clustering / Clustering-by-HNND-Pattern-Recognition-2023
Hierarchical Nearest Neighbor Descent, In-Tree, and Clustering (Teng Qiu, Yongjie Li, Pattern Recognition, 2023)
Language:R 0Very fast method to read number of events from some / all FCS files in a directory
Language:RR Script to plot the average event rate in flow or mass cytometry (FCS) files
Language:RA handy spreadsheet for looking up elemental isotopes by symbol or mass.
