R Observatory: Metrics for HetSeq version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HetSeq

0.1.1Package record

Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity

0packages depend

2.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Kevin BergCRAN page ↗GitHub ↗Issues ↗

Cellular responses to perturbations are highly heterogeneous and depend largely on the initial state of cells. Connecting post-perturbation cells via cellular trajectories to untreated cells (e.g. by leveraging metabolic labeling information) enables exploitation of intercellular heterogeneity as a combined knock-down and overexpression screen to identify pathway modulators, termed Heterogeneity-seq (see 'Berg et al' doi:10.1101/2024.10.28.620481). This package contains functions to generate cellular trajectories based on scSLAM-seq (single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing) time courses, functions to identify pathway modulators and to visualize the results.

Changes in 0.1.1

Initial CRAN Release

First release of the HetSeq package.
Provides tools for creating cell-cell trajectories.
Implements methods for identifying pathway modulators by leveraging intercellular heterogeneity.
Includes plot functions to visualize the results.

From NEWS.md in the release

Install

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

install.packages("HetSeq", 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("erhard-lab/HetSeq")

Development version from erhard-lab/HetSeq. 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-hetseq

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-HetSeq

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-HetSeq

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

13OK

CRAN check page ↗

Slowest check: 5.2 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-10

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMEYes · 1,018 wordsVignettesNoNEWSYes · 67% structured · mentions 0.1.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9
Examples that run: 0%8 never run
Exported functions with examples: 89%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #13,279 · ~7/day · ~213/mo

Releases R versions

Daily download trend is not available in this view yet.

29930 days

86590 days

2.6K1 year

Compare downloads with other packages →

Also on66 r2u2 autocran

How downloads are counted

Repository

erhard-lab/hetseq ↗Organization: erhard-lab

0Stars

0Forks

1Open issues

0Open PRs

0Releases

Last activity 2026-10-07

Responsiveness

not measured

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/erhard-lab/hetseq on 2026-10-21.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Automation and maintenance (1)

pre-commit

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing HetSeq adds 178 packages (105 with compiled code, 153 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1.0

Imports (17)

cowplot doParallel foreach DoubleML e1071 igraph ggplot2 ggrastr ggrepel grandR lpSolve mlr3 pROC reshape2 scales Seuratstats

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Kevin Berg

Author, Maintainer since 0.1.0 (2025)

Florian Erhard

Author

Lygeri Sakellaridi

Author

Releases (2)

Pick two releases to compare their code metrics.

0.1.1Latest
record
2026-06-01 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.1.0
record
2025-02-03
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-02-03
Total releases: 2 / 1 yrs
License: Apache License (>= 2)
Minimum R: ≥ 4.1.0
Download size: 14 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HetSeq")

Format

Berg, K., Erhard, F., & Sakellaridi, L. (2026). HetSeq: Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.HetSeq

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 HetSeq version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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