R Observatory: Metrics for twosigma version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

twosigma

1.0.2Package record

DE Analysis for Single-Cell RNA-Sequencing Data

0packages depend

2.8Kdownloads / year

0.0%test coverage

0/13flavors OK

Overview

About

Maintained by Eric Van BurenCRAN page ↗GitHub ↗Issues ↗

Implements the TWO-Component Single Cell Model-Based Association Method (TWO-SIGMA) for gene-level differential expression (DE) analysis and DE-based gene set testing of single-cell RNA-sequencing datasets. See Van Buren et al. (2020) doi:10.1002/gepi.22361 and Van Buren et al. (2021) doi:10.1101/2021.01.24.427979.

Changes in 1.0.2

This is the first CRAN release of twosigma!

From NEWS.md in the release

Install

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

install.packages("twosigma", 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("edvanburen/twosigma")

Development version from edvanburen/twosigma. 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-twosigma

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-twosigma

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-twosigma

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) twosigmag.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly

CRAN check page ↗

Slowest check: 2.6 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTE2026-06-09
ERROR12 NOTE, 1 ERROR2026-06-08
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.2

READMEYes · 1,643 wordsVignettesNoNEWSYes · 33% structured · mentions 1.0.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 8
Examples that run: 100%8 run in a plain check
Exported functions with examples: 100%
Documented parameters: 94%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #16,355 · ~8/day · ~237/mo

Releases R versions

Daily download trend is not available in this view yet.

32430 days

76590 days

2.8K1 year

Compare downloads with other packages →

Also on67 r2u3 autocran

How downloads are counted

Repository

edvanburen/twosigma ↗Account: edvanburen

10Stars

3Forks

0Open issues

0Open PRs

0Releases

188Commits

1Commit identities

188 commits · Last activity 2023-06-08 · +25% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 64
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-01-18 · 82026-09-26 · 9

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/edvanburen/twosigma on 2026-10-22.

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing twosigma adds 65 packages (35 with compiled code, 73 MB of source tarballs). Heaviest: stringi 11 MB, TH.data 8.2 MB, ggplot2 6.0 MB.

Depends (0)

none

Imports (7)

multcomp glmmTMBmethodspscl pbapplyparalleldoParallel

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (4)

Eric Van Buren

Author, Maintainer since 1.0.2 (2021)

Ming Hu

Author

Yun Li

Author

Di Wu

Author

Releases (1)

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
R
R 4.2.0 released · 2022-04-22
1.0.2Latest
record
2021-12-13 · current release
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-13
Total releases: 1 / 5 yrs
License: AGPL-3 OSI
Download size: 486 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("twosigma")

Format

Van Buren, E., Hu, M., Li, Y., & Wu, D. (2021). twosigma: DE Analysis for Single-Cell RNA-Sequencing Data (Version 1.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.twosigma

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 twosigma version 1.0.2 [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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