R Observatory: Metrics for FateID version 0.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

FateID

0.2.2Package record

Quantification of Fate Bias in Multipotent Progenitors

1packages depend

5.2Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Dominic GrünCRAN page ↗

Application of 'FateID' allows computation and visualization of cell fate bias for multi-lineage single cell transcriptome data. Herman, J.S., Sagar, Grün D. (2018) DOI:10.1038/nmeth.4662.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

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

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

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-fateid

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-FateID

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

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-FateID

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Dominic Grün <dominic.gruen@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Dominic",
                    family = "Grün",
                    role = c("aut", "cre"),
                    email = "dominic.gruen@gmail.com")
as necessary.

CRAN check page ↗

Slowest check: 3.4 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.2

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 18
Examples that run: 69%11 run in a plain check · 5 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 94%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 6%

Vignettes (1)

An introduction to FateID. HTML

How these are measured

Downloads

5.2K

CRAN downloads in the past year

Rank #7,106 · ~14/day · ~435/mo

Releases R versions

Daily download trend is not available in this view yet.

44730 days

1.2K90 days

5.2K1 year

Compare downloads with other packages →

Also on159 r2u9 autocran1.4K conda_forge525 bioconda

How downloads are counted

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing FateID adds 33 packages (22 with compiled code, 13 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, reticulate 1.6 MB.

Depends (1)

R >= 3.5.0

Imports (13)

graphicsgrDeviceslocfit matrixStats pheatmap princurve randomForest RColorBrewer Rtsne somstatsumaputils

LinkingTo (0)

none

Suggests (3)

DESeq2 knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

1indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

RaceID

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (1)

Dominic Grün

Maintainer since 0.0.9 (2017)

Releases (14)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.2.2Latest
record
2022-06-14 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
0.2.1
record
2021-10-05 · diff ↗
R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2021-04-07
0.2.0
record
2021-04-07 · diff ↗ ·
removed 1 export
dptTraj
archivedRemoved from CRAN
2021-03-18
check problems were not corrected in time
R
R 4.0.0 released · 2020-04-24
0.1.9
record
2019-09-21 · diff ↗
0.1.8
record
2019-09-02 · diff ↗ ·
added 1 export
plotexpressionProfile
R
R 3.6.0 released · 2019-04-26
0.1.7
record
2019-03-28 · diff ↗

Show 10 earlier eventsHide 10 earlier events

0.1.6
record
2019-02-27 · diff ↗
0.1.5
record
2018-11-13 · diff ↗
0.1.4
record
2018-08-07 · diff ↗
0.1.3
record
2018-07-27 · diff ↗
0.1.2
record
2018-07-05 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.1.1
record
2018-03-26 · diff ↗
0.1.0
record
2017-11-15 · diff ↗
0.0.9
record
2017-11-15
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-11-15
Total releases: 14 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 235 KB / 1 file
Download size: 2.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("FateID")

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 FateID version 0.2.2 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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