R Observatory: Metrics for singleCellHaystack version 1.0.3

Balamuta, James Joseph

singleCellHaystack

1.0.3

A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data

0packages depend

5Kdownloads / year

21.4%test coverage

13/13checks pass

Overview

About

Maintained by Alexis VandenbonFirst published 2020-07-016 releasesCRAN page ↗GitHub ↗

One key exploratory analysis step in single-cell genomics data analysis is the prediction of features with different activity levels. For example, we want to predict differentially expressed genes (DEGs) in single-cell RNA-seq data, spatial DEGs in spatial transcriptomics data, or differentially accessible regions (DARs) in single-cell ATAC-seq data. 'singleCellHaystack' predicts differentially active features in single cell omics datasets without relying on the clustering of cells into arbitrary clusters. 'singleCellHaystack' uses Kullback-Leibler divergence to find features (e.g., genes, genomic regions, etc) that are active in subsets of cells that are non-randomly positioned inside an input space (such as 1D trajectories, 2D tissue sections, multi-dimensional embeddings, etc). For the theoretical background of 'singleCellHaystack' we refer to our original paper Vandenbon and Diez (Nature Communications, 2020) doi:10.1038/s41467-020-17900-3 and our update Vandenbon and Diez (Scientific Reports, 2023) doi:10.1038/s41598-023-38965-2.

Install

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

install.packages("singleCellHaystack", 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("alexisvdb/singleCellHaystack")

Development version from alexisvdb/singleCellHaystack. 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-singlecellhaystack

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-singleCellHaystack

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-singleCellHaystack

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 4.6 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.03

21.4%

Coverage · measured lines

100%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 67%
References docs: 0%

Downloads

5K

CRAN downloads in the past year

Rank #8,581 · ~14/day · ~419/mo

Releases R versions

Daily download trend is not available in this view yet.

20330 days

1.1K90 days

5K1 year

Compare downloads with other packages →

Also on130 r2u5 autocran23 c2d4u

Repository

GitHub ↗ alexisvdb/singlecellhaystack

92Stars

9Forks

0Open issues

0Open PRs

0Releases

451Commits

3Contributors

bioinformaticssingle-cellrtranscriptomicsspatial-transcriptomicscite-seqpseudotimescatac-seq

451 commits · Last activity 2025-12-04 · +2.2% stars, 30d

Stars over time

2025-07-14 · 832026-08-05 · 92

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/alexisvdb/singlecellhaystack on 2026-08-03.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (5)

methodsMatrixsplinesggplot2 reshape2

LinkingTo (0)

none

Suggests (11)

knitr rmarkdown testthat SummarizedExperiment SingleCellExperiment SeuratObject cowplot wrswoR sparseMatrixStats ComplexHeatmap patchwork

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Alexis Vandenbon

Author, Maintainer

Authors (2)

Alexis Vandenbon

Author, Maintainer

Diego Diez

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.3Latest
2025-12-04 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.2
2024-01-11 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.0
2022-12-20 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.3.4
2021-03-28 · diff ↗
0.3.3
2020-09-18 · diff ↗
0.3.2
2020-07-01
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-07-01
Total releases: 6 / 6 yrs
License: MIT + file LICENSE OSI
Bundled data: 165 KB / 1 file
Download size: 1.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Start here. This is the citation for the package itself.

citation("singleCellHaystack")

CRAN DOI

https://doi.org/10.32614/CRAN.package.singleCellHaystack

BibTeX, derived from DESCRIPTION

@Manual{singleCellHaystack,
  title  = {singleCellHaystack: A Universal Differential Expression Prediction Tool for
Single-Cell and Spatial Genomics Data},
  author = {Vandenbon, Alexis and Diez, Diego},
  year   = {2025},
  note   = {R package version 1.0.3},
  doi    = {10.32614/CRAN.package.singleCellHaystack},
  url    = {https://CRAN.R-project.org/package=singleCellHaystack}
}

Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.

This is the citation for the package. It is not a citation for the R Observatory.

Cite this page

Use this when the claim is about a measurement on this page.

BibTeX

@misc{robservatorysingleCellHaystack,
  author    = {Balamuta, James Joseph},
  title     = {{R} {Observatory}: Metrics for {singleCellHaystack} version 1.0.3},
  year      = {2026},
  publisher = {HJJB, LLC},
  url       = {https://r-observatory.thecoatlessprofessor.com/packages/singleCellHaystack},
  note      = {Data set. Data release v2026-08-05}
}

APA

Balamuta, J. J. (2026). R Observatory: Metrics for singleCellHaystack version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/packages/singleCellHaystack

RIS

TY  - DATA
AU  - Balamuta, James Joseph
TI  - R Observatory: Metrics for singleCellHaystack version 1.0.3
PY  - 2026
PB  - HJJB, LLC
N1  - Data release v2026-08-05
UR  - https://r-observatory.thecoatlessprofessor.com/packages/singleCellHaystack
ER  -

In prose

These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/packages/singleCellHaystack.

Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.

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