cell_signatures: Cell type signatures
In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics
cell_signatures R Documentation
Cell type signatures
Description
Cell type signatures
Format
An object of class tmodGS
Details
* CellMarker: Zhang X, Lan Y, Xu J, Quan F, Zhao E, Deng C, Luo T, Xu L, Liao G, Yan M, Ping Y. CellMarker: a manually curated resource of cell markers in human and mouse. Nucleic acids research. 2019 Jan 8;47(D1):D721-8.
* CIBERSORT: Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA. Robust enumeration of cell subsets from tissue expression profiles. Nature methods. 2015 May;12(5):453-7.
* PanglaoDB: Franzén O, Gan LM, Björkegren JL. PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. Database. 2019 Jan 1;2019.
Source
CIBERSORT, CellMarkers, PanglaoDB
Examples
## to use cell signatures, type
data(cell_signatures)
data(vaccination)
gl <- vaccination$GeneName[ order(vaccination$qval.F.D1) ]
tmodCERNOtest(gl, mset=cell_signatures)
tmod documentation built on March 31, 2023, 9 p.m.
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| cell_signatures | R Documentation |
Cell type signatures
Description
Cell type signatures
Format
An object of class tmodGS
Details
* CellMarker: Zhang X, Lan Y, Xu J, Quan F, Zhao E, Deng C, Luo T, Xu L, Liao G, Yan M, Ping Y. CellMarker: a manually curated resource of cell markers in human and mouse. Nucleic acids research. 2019 Jan 8;47(D1):D721-8.
* CIBERSORT: Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA. Robust enumeration of cell subsets from tissue expression profiles. Nature methods. 2015 May;12(5):453-7.
* PanglaoDB: Franzén O, Gan LM, Björkegren JL. PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. Database. 2019 Jan 1;2019.
Source
CIBERSORT, CellMarkers, PanglaoDB
Examples
## to use cell signatures, type
data(cell_signatures)
data(vaccination)
gl <- vaccination$GeneName[ order(vaccination$qval.F.D1) ]
tmodCERNOtest(gl, mset=cell_signatures)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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