top.markers

Number of top differentially expressed genes to be choosen from each cluster, default = 10.

topde

Minimum base mean of the genes to be chosen, default = 0.5.

min.base.mean

Filter markers that are seen for more than one cluster, default = TRUE.

filt.ambig

Choose a cluster to find markers for. If 0, it would find markers for all clusters, , default = 0.

cluster

This function takes the marker genes info if chooses marker gene names for plots.

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

top.markers function

<dl><dt>x</dt>
<dd>An object of class iCellR.</dd>
<dt>topde</dt>
<dd>Number of top differentially expressed genes to be choosen from each cluster, default = 10.</dd>
<dt>min.base.mean</dt>
<dd>Minimum base mean of the genes to be chosen, default = 0.5.</dd>
<dt>filt.ambig</dt>
<dd>Filter markers that are seen for more than one cluster, default = TRUE.</dd>
<dt>cluster</dt>
<dd>Choose a cluster to find markers for. If 0, it would find markers for all clusters, , default = 0.</dd></dl>

Arguments

Choose top marker genes — top.markers

<dl>

<dt>x</dt>
<dd>An object of class iCellR.</dd>


<dt>topde</dt>
<dd>Number of top differentially expressed genes to be choosen from each cluster, default = 10.</dd>


<dt>min.base.mean</dt>
<dd>Minimum base mean of the genes to be chosen, default = 0.5.</dd>


<dt>filt.ambig</dt>
<dd>Filter markers that are seen for more than one cluster, default = TRUE.</dd>


<dt>cluster</dt>
<dd>Choose a cluster to find markers for. If 0, it would find markers for all clusters, , default = 0.</dd>

</dl>

top.markers: Choose top marker genes

Description

Usage

Value

Arguments