iCellR

1.7.0

Analyzing High-Throughput Single Cell Sequencing Data

0packages depend

5.9Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Alireza Khodadadi-JamayranFirst published 2019-08-0225 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)

install.packages("iCellR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("rezakj/iCellR")

Development version from rezakj/iCellR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-icellr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-iCellR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 6.1 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 3 earlier snapshots

OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 97%
References docs: 1%

Downloads

5.9K

CRAN downloads in the past year

Rank #8,265 · ~16/day · ~489/mo

Releases R versions

Daily download trend is not available in this view yet.

35130 days

1.2K90 days

5.9K1 year

Compare downloads with other packages →

Also on442 r2u299 conda_forge48 c2d4u

Repository

GitHub ↗ rezakj/icellr

126Stars

19Forks

0Open issues

1Open PRs

11Releases

136Commits

5Contributors

singel-cell-sequencingclustering-algorithmclusteringnormalizationumappseudotimescrna-seqscvdj-seq

136 commits · Last activity 2025-11-10 · 0% stars, 30d

Stars over time

2025-03-13 · 1202026-07-07 · 126

Repository practices

Upstream repositoryBeta

Checks run against github.com/rezakj/icellr on 2026-07-31.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

28 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.3.0ggplot2 plotly

Imports (27)

MatrixRtsne gridExtra ggrepel ggpubr scatterplot3d RColorBrewer knitr NbClust shiny pheatmap ape ggdendro plyr reshape Hmisc htmlwidgetsmethodsuwot progress igraph data.table Rcpp hdf5r RANN jsonlite png

LinkingTo (1)

Rcpp

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (8)

Maintainer (1)

Alireza Khodadadi-Jamayran

Author, Maintainer

Authors (8)

Alireza Khodadadi-Jamayran

Author, Maintainer

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Contributors (7)

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Package Timeline

25 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.7.0Latest
2025-10-28 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.6.7
2024-01-29 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.6.5
2021-10-09 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.6.4
2021-04-27 · diff ↗
1.6.1
2021-03-04 · diff ↗
1.6.0
2021-01-30 · diff ↗
1.5.9
2021-01-21 · diff ↗
1.5.8
2020-10-09 · diff ↗
1.5.5
2020-07-16 · diff ↗
1.5.4
2020-07-03 · diff ↗

Show 17 earlier events

1.5.1
2020-06-17 · diff ↗
1.5.0
2020-05-08 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.4.5
2020-04-10 · diff ↗
1.4.0
2020-04-03 · diff ↗
1.3.3
2020-03-14 · diff ↗
1.3.1
2020-02-26 · diff ↗
1.3.0
2020-01-24 · diff ↗
1.2.9
2020-01-17 · diff ↗
1.2.7
2019-12-04 · diff ↗
1.2.5
2019-11-04 · diff ↗
1.2.2
2019-10-22 · diff ↗
1.2.0
2019-10-15 · diff ↗
1.1.4
2019-09-26 · diff ↗
1.1.2
2019-09-10 · diff ↗
1.0.0
2019-08-02
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-02
Total releases: 25 / 7 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.3.0
Bundled data: 0.6 KB / 2 files
Download size: 221 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Missing Data Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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