Package: iCellR
Type: Package
Title: Analyzing High-Throughput Single Cell Sequencing Data
Version: 1.7.0
Authors@R: c(
  person(given = 'Alireza', family = 'Khodadadi-Jamayran',role = c('aut','cre'), email = 'alireza.khodadadi.j@gmail.com', comment = c(ORCID = '0000-0003-2495-7504')),
  person(given = 'Joseph', family = 'Pucella',role = c('aut','ctb'), comment = c(ORCID = '0000-0003-0875-8046')),
  person(given = 'Hua', family = 'Zhou',role = c('aut','ctb'), comment = c(ORCID = '0000-0003-1822-1306')),
  person(given = 'Nicole', family = 'Doudican',role = c('aut','ctb'), comment = c(ORCID = '0000-0003-3827-9644')),
  person(given = 'John', family = 'Carucci',role = c('aut','ctb'), comment = c(ORCID = '0000-0001-6817-9439')),
  person(given = 'Adriana', family = 'Heguy',role = c('aut','ctb')),
  person(given = 'Boris', family = 'Reizis',role = c('aut','ctb'), comment = c(ORCID = '0000-0003-1140-7853')),
  person(given = "Aristotelis", family = "Tsirigos",role = c('aut','ctb'), comment = c(ORCID = '0000-0002-7512-8477'))
  )
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j@gmail.com>
Description: 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.
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, progress,
        igraph, data.table, Rcpp, hdf5r, RANN, jsonlite, png
License: GPL-2
LinkingTo: Rcpp
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.2
BugReports: https://github.com/rezakj/iCellR/issues
URL: https://github.com/rezakj/iCellR
NeedsCompilation: yes
Packaged: 2026-10-06 10:28:46 UTC; root
Author: Alireza Khodadadi-Jamayran [aut, cre]
        (<https://orcid.org/0000-0003-2495-7504>), Joseph Pucella [aut,
        ctb] (<https://orcid.org/0000-0003-0875-8046>), Hua Zhou [aut,
        ctb] (<https://orcid.org/0000-0003-1822-1306>), Nicole Doudican
        [aut, ctb] (<https://orcid.org/0000-0003-3827-9644>), John
        Carucci [aut, ctb] (<https://orcid.org/0000-0001-6817-9439>),
        Adriana Heguy [aut, ctb], Boris Reizis [aut, ctb]
        (<https://orcid.org/0000-0003-1140-7853>), Aristotelis Tsirigos
        [aut, ctb] (<https://orcid.org/0000-0002-7512-8477>)
Config/pak/sysreqs: cmake libglpk-dev make libhdf5-dev libicu-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://rezakj.r-universe.dev
Date/Publication: 2025-11-10 15:27:23 UTC
RemoteUrl: https://github.com/rezakj/icellr
RemoteRef: HEAD
RemoteSha: 4a1c8ba9c49bf804e1cc87e51b7a61936d3c452b