Cytofkit specifications

Information


Unique identifier OMICS_12995
Name Cytofkit
Interface Web user interface
Restrictions to use None
Input data Rdata
Programming languages R
License Artistic License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

Download


Documentation


Maintainer


  • person_outline Jinmiao Chen <>

Information


Unique identifier OMICS_12995
Name Cytofkit
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data FCS data
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.12.0
Stability Stable
Requirements
methods, stats, plyr, gplots, parallel, graphics, BiocGenerics, Biobase, utils, testthat, grDevices, ggplot2, ggrepel, RUnit, knitr, reshape2, VGAM, tcltk, shiny, R(>=3.4.0), doParallel, e1071, pdist, flowCore, vegan, colourpicker, Rtsne, destiny, shinyFiles, FlowSOM(>=1.4.0), igraph(>=1.1.2), RANN(>=2.5), Rcpp(>=0.12.0)
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Jinmiao Chen <>

Publications for Cytofkit

Cytofkit in publications

 (9)
PMCID: 5919961
PMID: 29731749
DOI: 10.3389/fimmu.2018.00686

[…] that optimally locates cells with similar expression levels near to each other and cells with dissimilar expression levels further apart. tsne analysis were performed using custom r scripts and cytofkit software (). statistical analysis: groups of hcmv-seronegative and hcmv-seropositive donors were analyzed by mann–whitney u test to compare values. the wilcoxon matched-pairs signed rank […]

PMCID: 5854609
PMID: 29545564
DOI: 10.1038/s41467-018-03301-0

[…] min. fcs files were concatenated and normalized using the cytobank concatenation tool and matlab normalizer, respectively. data were processed and analyzed with cytobank and r using the opencyto and cytofkit packages., cytokines measurement of culture supernatants was performed using the human th1/th2 10-plex tissue culture kit from msd platform. supernatants of 96-well culture plates […]

PMCID: 5754202
PMID: 29299998
DOI: 10.7554/eLife.30947.018

[…] reduction using 13 parameters, (ly6c, ym1, cd11b, cd115, pdl-2, gata6, tim4, relma, mhc-ii, cd11c, f4/80 forward-scatter area and side scatter area) was performed using the bioconductor r package, cytofkit and fcs files were exported for analysis in flowjo., statistical significance on data from naïve and infected c57bl/6 and balb/c mice, was carried out using a two way-anova. when data […]

PMCID: 5772172
PMID: 29262348
DOI: 10.1016/j.immuni.2017.11.024

[…] dna intercalating fraction) and dead cells (cisplatin+). myeloid cd45+lin(cd3+cd7+cd15+cd19+cd20+cd56)- cells were exported and used for analysis. downstream analysis was performed using the cytofkit r package. for comparison of the different differentiating conditions data from 1000 myeloid cells was randomly sampled per donor and condition (3 donors; 12,000 cells in total) […]

PMCID: 5715069
PMID: 29203769
DOI: 10.1038/s41467-017-01963-w

[…] **p ≤ 0.01; ***p ≤ 0.001., equal numbers of γδ t cells were down-sampled from each replicate, concatenated to a single fcs file using flowjo and used for analysis in r using the 'flowcore' and 'cytofkit' packages, . t-sne was calculated for 10,000 cells based on the expression of cd24, cd25, cd73, cd117, cd200 and cd371. due to the stochasticity of the algorithm, multiple t-sne graphs […]


To access a full list of publications, you will need to upgrade to our premium service.

Cytofkit institution(s)
Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore
Cytofkit funding source(s)
This study was funded by A-STAR/SIgN core funding.

Cytofkit reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Cytofkit