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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

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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


No version available

Documentation


Maintainer


  • person_outline Jinmiao Chen

Publications for Cytofkit

Cytofkit citations

 (13)
library_books

Adaptive NKG2C+CD57+ Natural Killer Cell and Tim 3 Expression During Viral Infections

2018
Front Immunol
PMCID: 5919961
PMID: 29731749
DOI: 10.3389/fimmu.2018.00686

[…] ethod 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 test […]

library_books

Sensitive and frequent identification of high avidity neo epitope specific CD8+ T cells in immunotherapy naive ovarian cancer

2018
Nat Commun
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. […]

library_books

Comparison of CyTOF assays across sites: Results of a six center pilot study

2018
J Immunol Methods
PMCID: 5805584
PMID: 29174717
DOI: 10.1016/j.jim.2017.11.008

[…] chnical batch effect exists between centers. Similarly, calculating a PCA of all samples prepared by each center, highlights that samples are comparable in a high-dimensional setting.Next, SPADE3 and Cytofkit (FlowSOM, ClusterX, and Rphenograph) analyses were performed on the same harmonized MATLAB-normalized files. The same 14 surface markers were used for clustering in both SPADE3 and Cytofkit ( […]

library_books

Myeloid cell recruitment versus local proliferation differentiates susceptibility from resistance to filarial infection

2018
eLife
PMCID: 5754202
PMID: 29299998
DOI: 10.7554/eLife.30947.018

[…] ty 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. […]

library_books

Cellular Differentiation of Human Monocytes Is Regulated by Time Dependent Interleukin 4 Signaling and the Transcriptional Regulator NCOR2

2017
Immunity
PMCID: 5772172
PMID: 29262348
DOI: 10.1016/j.immuni.2017.11.024

[…] -191/193 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) and autoLgcl- […]

library_books

Three distinct developmental pathways for adaptive and two IFN γ producing γδ T subsets in adult thymus

2017
Nat Commun
PMCID: 5715069
PMID: 29203769
DOI: 10.1038/s41467-017-01963-w

[…] ed on the mean expression of cells within each cluster. Progression analysis was conducted using the Isomap and Diffusionmap algorithms on a cluster-based down-sampled data set, as recommended in the cytofkit manual. […]

Citations

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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.

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