iCellR: Analyzing High-Throughput Single Cell Sequencing Data

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.

Version: 1.6.7
Depends: R (≥ 3.3.0), ggplot2, plotly
Imports: Matrix, Rtsne, gridExtra, ggrepel, ggpubr, scatterplot3d, RColorBrewer, knitr, NbClust, shiny, pheatmap, ape, ggdendro, plyr, reshape, Hmisc, htmlwidgets, methods, uwot, hdf5r, progress, igraph, data.table, Rcpp, RANN, jsonlite, png
LinkingTo: Rcpp
Published: 2024-01-29
DOI: 10.32614/CRAN.package.iCellR
Author: Alireza Khodadadi-Jamayran ORCID iD [aut, cre], Joseph Pucella ORCID iD [aut, ctb], Hua Zhou ORCID iD [aut, ctb], Nicole Doudican ORCID iD [aut, ctb], John Carucci ORCID iD [aut, ctb], Adriana Heguy [aut, ctb], Boris Reizis ORCID iD [aut, ctb], Aristotelis Tsirigos ORCID iD [aut, ctb]
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j at>
License: GPL-2
NeedsCompilation: yes
Citation: iCellR citation info
In views: MissingData, Omics
CRAN checks: iCellR results


Reference manual: iCellR.pdf


Package source: iCellR_1.6.7.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): iCellR_1.6.7.tgz, r-oldrel (arm64): iCellR_1.6.7.tgz, r-release (x86_64): iCellR_1.6.7.tgz, r-oldrel (x86_64): iCellR_1.6.7.tgz
Old sources: iCellR archive

Reverse dependencies:

Reverse imports: MAPFX


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