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bioc
flowPloidy:Analyze flow cytometer data to determine sample ploidy
Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.
Maintained by Tyler Smith. Last updated 5 months ago.
flowcytometryguiregressionvisualizationbioconductorevolutionflow-cytometrypolyploidy
5 stars 6.26 score 5 scripts
gitdemont
IFC:Tools for Imaging Flow Cytometry
Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Maintained by Yohann Demont. Last updated 25 days ago.
cytometrycytometry-dataflowflow-cytometryflow-cytometry-analysisflow-cytometry-dataflow-cytometry-filesifcimageimaging-flow-cytometryimaging-flow-cytometry-datamicroscopycpp
4 stars 5.34 score 12 scripts
lance-waller-lab
gateR:Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Estimates statistically significant marker combination values within which one immunologically distinctive group (i.e., disease case) is more associated than another group (i.e., healthy control), successively, using various combinations (i.e., "gates") of markers to examine features of cells that may be different between groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk function estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Maintained by Ian D. Buller. Last updated 1 years ago.
cytometryflow-cytometrygatingkernel-density-estimationmass-cytometrynon-euclidean-spacesspatial-analysis
2 stars 4.00 score 6 scripts