qc.stats

This function takes data frame and calculates the number of UMIs, genes per cell and percentage of mitochondrial genes per cell and cell cycle genes.

A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST). Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more details.

Alireza Khodadadi-Jamayran

iCellR

Analyzing High-Throughput Single Cell Sequencing Data

Joseph Pucella

Hua Zhou

Nicole Doudican

John Carucci

Adriana Heguy

Boris Reizis

Aristotelis Tsirigos

qc.stats function

<dl><dt>x</dt>
<dd>A data frame containing gene counts for cells.</dd>
<dt>which.data</dt>
<dd>Choose from "raw.data" or "main.data", "imputed.data", default = "raw.data".</dd>
<dt>mito.genes</dt>
<dd>A character vector of mitochondrial genes names , default is the genes starting with mt.</dd>
<dt>s.phase.genes</dt>
<dd>A character vector of gene names for S phase, default = s.phase.</dd>
<dt>g2m.phase.genes</dt>
<dd>A character vector of gene names for G2 and M phase, default = g2m.phase.</dd></dl>

Arguments

Calculate the number of UMIs and genes per cell and percentage of mitochondrial genes per cell and cell cycle genes. — qc.stats

<dl>

<dt>x</dt>
<dd>A data frame containing gene counts for cells.</dd>


<dt>which.data</dt>
<dd>Choose from "raw.data" or "main.data", "imputed.data", default = "raw.data".</dd>


<dt>mito.genes</dt>
<dd>A character vector of mitochondrial genes names , default is the genes starting with mt.</dd>


<dt>s.phase.genes</dt>
<dd>A character vector of gene names for S phase, default = s.phase.</dd>


<dt>g2m.phase.genes</dt>
<dd>A character vector of gene names for G2 and M phase, default = g2m.phase.</dd>

</dl>

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qc.stats: Calculate the number of UMIs and genes per cell and percentage of mitochondrial genes per cell and cell cycle genes.

Description

Usage

Value

Arguments