HetSeq

0.1.1

Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity

0packages depend

2.2Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Kevin BergFirst published 2025-02-032 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

1NOTE12OK

Failing flavors

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

Slowest check: 5.7 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
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,018 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

2.2K

CRAN downloads in the past year

Rank #13,564 · ~6/day · ~180/mo

Releases R versions

Daily download trend is not available in this view yet.

18130 days

75790 days

2.2K1 year

Compare downloads with other packages →

Also on88 r2u

Repository

GitHub ↗ erhard-lab/hetseq

0Stars

0Forks

1Open issues

0Open PRs

0Releases

Last activity 2026-05-29

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/erhard-lab/hetseq on 2026-07-31.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (3)

Maintainer (1)

Kevin Berg

Author, Maintainer

Authors (3)

Kevin Berg

Author, Maintainer

Florian Erhard

Author

Lygeri Sakellaridi

Author

Package Timeline

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

0.1.1Latest
2026-06-01 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.1.0
2026-03-10
R
R 4.5.0 released · 2025-04-11

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
Installed size: not tracked yet
With dependencies: not tracked yet

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