iCellR

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Software:120377



CRANiCellRMaRDI QIDQ120377

Analyzing High-Throughput Single Cell Sequencing Data

Alireza Khodadadi-Jamayran, Joseph N Pucella, Hua Zhou, Nicole Doudican, John Carucci, Adriana Heguy, Boris Reizis, Aristotelis Tsirigos

Last update: 29 January 2024

Software version identifier: 1.6.5, 1.0.0, 1.1.2, 1.1.4, 1.2.0, 1.2.2, 1.2.5, 1.2.7, 1.2.9, 1.3.0, 1.3.1, 1.3.3, 1.4.0, 1.4.5, 1.5.0, 1.5.1, 1.5.4, 1.5.5, 1.5.8, 1.5.9, 1.6.0, 1.6.1, 1.6.4, 1.6.7


Copyright license: GNU General Public License, version 2.0

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.