R Observatory: Metrics for iCellR version 1.7.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

iCellR

1.7.0Package record

Analyzing High-Throughput Single Cell Sequencing Data

0packages depend

5.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Alireza Khodadadi-JamayranCRAN page ↗GitHub ↗Issues ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

13OK

CRAN check page ↗

Slowest check: 4.9 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-13
ERROR12 OK, 1 ERROR2026-08-13
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-04-10
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.7.0

READMENoVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 69
Examples that run: 100%3 run in a plain check
Exported functions with examples: 4%
Documented parameters: 100%
Return-value docs: 97%
Help pages citing references: 1%

How these are measured

Downloads

5.7K

CRAN downloads in the past year

Rank #5,916 · ~16/day · ~472/mo

Releases R versions

Daily download trend is not available in this view yet.

56530 days

1.4K90 days

5.7K1 year

Compare downloads with other packages →

Also on412 r2u382 conda_forge91 c2d4u

How downloads are counted

Repository

rezakj/icellr ↗Account: rezakj

126Stars

19Forks

0Open issues

1Open PRs

11Releases

136Commits

5Commit identities

singel-cell-sequencingclustering-algorithmclusteringnormalizationumappseudotimescrna-seqscvdj-seq

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

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 48
Median days to close, 50 most recently updated closed PRs: 385

Stars over time

2025-08-31 · 1212026-07-07 · 126

How these are measured

PracticesBeta

Checks run against github.com/rezakj/icellr on 2026-10-11.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

28 external dependencies (excludes base and recommended)

Installing iCellR adds 138 packages (73 with compiled code, 129 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (8)

Alireza Khodadadi-Jamayran

Author, Maintainer since 1.0.0 (2019)

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Releases (25)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.7.0Latest
record
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
record
2024-01-29 · diff ↗ ·
added 1 export
bubble.gg.plot
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.6.5
record
2021-10-09 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.6.4
record
2021-04-27 · diff ↗ ·
added 1 export
make.bed
1.6.1
record
2021-03-04 · diff ↗ ·
added 1 export
i.score
1.6.0
record
2021-01-30 · diff ↗ ·
added 3 exports
add.10x.image, capture.image.10x, spatial.plot
1.5.9
record
2021-01-21 · diff ↗
1.5.8
record
2020-10-09 · diff ↗
1.5.5
record
2020-07-16 · diff ↗ ·
added 1 export
pseudotime.knetl
1.5.4
record
2020-07-03 · diff ↗ ·
added 3 exports
Rphenograph, clust.ord, find_neighbors

Show 17 earlier eventsHide 17 earlier events

1.5.1
record
2020-06-17 · diff ↗ ·
added 1 export
cell.cycle
1.5.0
record
2020-05-08 · diff ↗ ·
added 1 export
run.knetl
R
R 4.0.0 released · 2020-04-24
1.4.5
record
2020-04-10 · diff ↗ ·
added 1 export
iclust
1.4.0
record
2020-04-03 · diff ↗ ·
added 1 export
iba
1.3.3
record
2020-03-14 · diff ↗
1.3.1
record
2020-02-26 · diff ↗
1.3.0
record
2020-01-24 · diff ↗ ·
added 1 export
load.h5
1.2.9
record
2020-01-17 · diff ↗
1.2.7
record
2019-12-04 · diff ↗
1.2.5
record
2019-11-04 · diff ↗ ·
added 1 export
run.anchor
1.2.2
record
2019-10-22 · diff ↗ ·
added 1 export
run.mnn
1.2.0
record
2019-10-15 · diff ↗
1.1.4
record
2019-09-26 · diff ↗ ·
added 1 export
run.phenograph
1.1.2
record
2019-09-10 · diff ↗ ·
added 1 export
hto.anno
1.0.0
record
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

Appears in task views

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

Cite

Cite this package

Run in R for the authors' entry:

citation("iCellR")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1101/2020.03.31.019109.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for iCellR version 1.7.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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