FateID (version 0.2.2)

Quantification of Fate Bias in Multipotent Progenitors

Description

Application of 'FateID' allows computation and visualization of cell fate bias for multi-lineage single cell transcriptome data. Herman, J.S., Sagar, Grn D. (2018) .

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Version

Install

install.packages('FateID')

Monthly Downloads

288

Version

0.2.2

License

GPL-3

Maintainer

Dominic Grc3<bc>n

Last Published

June 14th, 2022

Functions in FateID (0.2.2)

diffexpnb

Function for differential expression analysis

plotexpressionProfile

Plotting smoothed pseudo-temporal expression profiles for groups of genes

plotexpression

Plotting of pseudo-temporal expression profiles

procsom

Processing of self-organizing maps for pseudo-temporal expression profiles

reclassify

Reclassification of cells

prcurve

Computation of a principal curve for a given dimensional reduction representation

plotheatmap

Heatmap of expression profiles

plotFateMap

Plot dimensional reduction representation of the expression data

plotdiffgenesnb

Function for plotting differentially expressed genes

impGenes

Extract genes with high importance values for random forest classification

gene2gene

Comparative plot of the expression levels of two genes

getPart

Inference of a cell type partition

intestine

Single-cell transcriptome data of intestinal epithelial cells

compdr

Computation of dimensional reduction representations

getFeat

Feature selection based on differentially expressed genes

getsom

Topological ordering of pseudo-temporal expression profiles

fateBias

Computation of fate bias

filterset

Function for filtering expression data