Package: FateID 0.2.2

FateID: Quantification of Fate Bias in Multipotent Progenitors

Application of 'FateID' allows computation and visualization of cell fate bias for multi-lineage single cell transcriptome data. Herman, J.S., Sagar, Grün D. (2018) <doi:10.1038/nmeth.4662>.

Authors:Dominic Grün <[email protected]>

FateID_0.2.2.tar.gz
FateID_0.2.2.zip(r-4.7)FateID_0.2.2.zip(r-4.6)FateID_0.2.2.zip(r-4.5)
FateID_0.2.2.tgz(r-4.6-any)FateID_0.2.2.tgz(r-4.5-any)
FateID_0.2.2.tar.gz(r-4.7-any)FateID_0.2.2.tar.gz(r-4.6-any)
FateID_0.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
FateID/json (API)

# Install 'FateID' in R:

install.packages('FateID', repos = c('https://dgrun.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dgrun/fateid/issues

Datasets:

intestine - Single-cell transcriptome data of intestinal epithelial cells

On CRAN:

6.59 score 23 stars 1 packages 57 scripts 309 downloads 2 mentions 17 exports 35 dependencies

Last updated from:f2ea6f9b49. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	201
source / vignettes	OK	274
linux-release-x86_64	OK	193
macos-release-arm64	OK	191
macos-oldrel-arm64	OK	196
windows-devel	OK	138
windows-release	OK	160
windows-oldrel	OK	155
wasm-release	OK	140

Exports:compdr diffexpnb fateBias filterset gene2gene getFeat getPart getsom impGenes plotdiffgenesnb plotexpression plotexpressionProfile plotFateMap plotheatmap prcurve procsom reclassify

Dependencies:askpass cli farver glue gtable here jsonlite labeling lattice lifecycle locfit Matrix matrixStats openssl pheatmap png princurve R6 randomForest rappdirs RColorBrewer Rcpp RcppEigen RcppTOML reticulate rlang rprojroot RSpectra Rtsne scales som sys umap viridisLite withr

FateID reference manual

Rendered fromFateID.Rmdusingknitr::rmarkdown

Last update: 2022-06-14
Started: 2017-11-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Computation of dimensional reduction representations	compdr
Function for differential expression analysis	diffexpnb
Computation of fate bias	fateBias
Function for filtering expression data	filterset
Comparative plot of the expression levels of two genes	gene2gene
Feature selection based on differentially expressed genes	getFeat
Inference of a cell type partition	getPart
Topological ordering of pseudo-temporal expression profiles	getsom
Extract genes with high importance values for random forest classification	impGenes
Single-cell transcriptome data of intestinal epithelial cells	intestine
Function for plotting differentially expressed genes	plotdiffgenesnb
Plotting of pseudo-temporal expression profiles	plotexpression
Plotting smoothed pseudo-temporal expression profiles for groups of genes	plotexpressionProfile
Plot dimensional reduction representation of the expression data	plotFateMap
Heatmap of expression profiles	plotheatmap
Computation of a principal curve for a given dimensional reduction representation	prcurve
Processing of self-organizing maps for pseudo-temporal expression profiles	procsom
Reclassification of cells	reclassify