| Type: | Package |
| Title: | Profiling of Peripheral Blood Mononuclear Cells using CyTOF |
| Version: | 0.1.1 |
| Depends: | R (≥ 3.1.0) |
| Suggests: | ggplot2, cytofan, dplyr, reshape2, RColorBrewer, knitr, rmarkdown |
| Description: | This data package contains a subset of the Bodenmiller et al, Nat Biotech 2012 dataset for testing single cell, high dimensional analysis and visualization methods. |
| License: | CC0 |
| Encoding: | UTF-8 |
| LazyData: | TRUE |
| LazyDataCompression: | xz |
| URL: | https://github.com/yannabraham/bodenmiller |
| BugReports: | https://github.com/yannabraham/bodenmiller/issues |
| VignetteBuilder: | knitr |
| RoxygenNote: | 7.1.1 |
| NeedsCompilation: | no |
| Packaged: | 2021-04-11 14:20:25 UTC; ayann |
| Author: | Yann Abraham [aut, cre], Bernd Bodenmiller [aut] |
| Maintainer: | Yann Abraham <yann.abraham@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2021-04-11 15:20:06 UTC |
Reference Annotation
Description
A data.frame containing the source file and cell type for every cell in
refPhenoMat and refFuncMat. See
Bodenmiller et al 2012
for details.
Usage
refAnnots
Format
a data.frame with 15792 rows and 2 variables:
Sourcethe name of the source (fcs) file
Cellsthe cell type for the corresponding row in
refPhenoMatorrefFuncMat
Source
https://reports.cytobank.org/105/v2/
Reference Matrix (Functional)
Description
a matrix containing the signal intensity for functional markers measured using CyTOF
on different cell types. See
Bodenmiller et al 2012
for details.
Usage
refFuncMat
Format
a matrix with 15792 rows and 14 variables:
pStat1
pSlp76
pBtk
pPlcg2
pErk
pLat
pS6
pNFkB
pp38
pStat5
pAkt
pSHP2
pZap70
pStat3
Source
https://reports.cytobank.org/105/v2/
Reference Matrix (Phenotypic)
Description
a matrix containing the signal intensity for phenotypic markers measured using CyTOF
on different cell types. See
Bodenmiller et al 2012
for details.
Usage
refPhenoMat
Format
a matrix with 15792 rows and 9 variables:
CD20
IgM
CD4
CD33
HLA-DR
CD14
CD7
CD3
CD123
Source
https://reports.cytobank.org/105/v2/
Untreated Samples with 4 Different Treatments (Annotation)
Description
A data.frame containing the source file, cell type and stimulation for every cell in
refPhenoMat and refFuncMat.
Stimulations include BCR/FcR-XL, PMA/Ionomycin and vanadate.See
Bodenmiller et al 2012
for details.
Usage
untreatedAnnots
Format
a data.frame with 15792 rows and 2 variables:
Sourcethe name of the source (fcs) file
Treatmentthe treatment for the corresponding row in
refPhenoMatorrefFuncMatCellsthe cell type for the corresponding row in
refPhenoMatorrefFuncMat
Source
https://reports.cytobank.org/105/v2/
Untreated Samples with 4 Different Treatments (Functional)
Description
a matrix containing the signal intensity for functional markers measured using CyTOF
on different cell types, after stimulation with BCR/FcR-XL, PMA/Ionomycin
and vanadate. See
Bodenmiller et al 2012
for details.
Usage
untreatedFuncMat
Format
a matrix with 15792 rows and 14 variables:
pStat1
pSlp76
pBtk
pPlcg2
pErk
pLat
pS6
pNFkB
pp38
pStat5
pAkt
pSHP2
pZap70
pStat3
Source
https://reports.cytobank.org/105/v2/
Untreated Samples with 4 Different Treatments (Phenotypic)
Description
a matrix containing the signal intensity for phenotypic markers measured using CyTOF
on different cell types, after stimulation with BCR/FcR-XL, PMA/Ionomycin
and vanadate. See
Bodenmiller et al 2012
for details.
Usage
untreatedPhenoMat
Format
a matrix with 15792 rows and 9 variables:
CD20
IgM
CD4
CD33
HLA-DR
CD14
CD7
CD3
CD123