fitGammaRt

This function fits a Gamma distribution to the total transcript counts distribution across a given group of cells. Total transcript counts are normalized by the mean total transcript count across the group. This function is used to infer a Gamma distribution of the global cell-to-cell variability across pruned nearest neighbourhoods.

Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <DOI:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <DOI:10.1186/s13059-023-02974-1>).

Dominic Grc3<bc>n

RaceID

Identification of Cell Types, Inference of Lineage Trees, and
Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Dominic Grün

fitGammaRt function

<dl><dt>x</dt>
<dd>Transcript count matrix with cells as columns and genes as rows.</dd></dl>

Arguments

Fitting a Gamma distribution to global cell-to-cell variability — fitGammaRt

<dl>

<dt>x</dt>
<dd>Transcript count matrix with cells as columns and genes as rows.</dd>

</dl>

fitGammaRt: Fitting a Gamma distribution to global cell-to-cell variability

Description

Usage

Value

Arguments