R Observatory: Metrics for pagoda2 version 1.0.15

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pagoda2

1.0.15Package record

Single Cell Analysis and Differential Expression

1packages dependsuggested by 2

8.8Kdownloads / year

0.6%test coverage

11/13flavors OK

Overview

About

Maintained by Evan BiederstedtCRAN page ↗GitHub ↗Issues ↗

Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, https://github.com/kharchenkolab/conos. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at https://github.com/kharchenkolab/pagoda2. The size of the 'p2data' package is approximately 6 MB.

Install

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

install.packages("pagoda2", 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("kharchenkolab/pagoda2")

Development version from kharchenkolab/pagoda2. 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-pagoda2

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-pagoda2

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-pagoda2

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

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘pagoda2WebApp_arrayToJSON.Rd’ ‘pagoda2WebApp_call.Rd’
  ‘pagoda2WebApp_generateDendrogramOfGroups.Rd’
  ‘pagoda2WebApp_generateGeneKnnJSON.Rd’
  ‘pagoda2WebApp_getCompressedEmbedding.Rd’
  ‘pagoda2WebApp_packCompressFloat64Array.Rd’
  ‘pagoda2WebApp_packCompressInt32Array.Rd’
  ‘pagoda2WebApp_readStaticFile.Rd’
  ‘pagoda2WebApp_serializeToStaticFast.Rd’ ‘pagoda2WebApp_serverLog.Rd’
  ‘pagoda2WebApp_sparseMatList.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 6.5 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE10 OK, 2 NOTE2026-04-10

Show 2 earlier changesHide 2 earlier changes

ERROR9 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.15

READMEYes · 457 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 89 (16 internal)
Examples that run: 50%2 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 7%
Documented parameters: 100%
Return-value docs: 93%
Help pages citing references: 0%

How these are measured

Downloads

8.8K

CRAN downloads in the past year

Rank #3,375 · ~24/day · ~732/mo

Releases R versions

Daily download trend is not available in this view yet.

1.3K30 days

3.3K90 days

8.8K1 year

Compare downloads with other packages →

Also on633 r2u8 autocran3.8K conda_forge43 c2d4u

How downloads are counted

Repository

kharchenkolab/pagoda2 ↗Organization: kharchenkolab

262Stars

46Forks

2Open issues

0Open PRs

19Releases

1,491Commits

17Commit identities

single-celltranscriptomicsscrna-seqsingle-cell-rna-seq

1,491 commits · Last activity 2026-04-01 · +1.2% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 82%
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-10-14 · 2372026-10-07 · 262

How these are measured

PracticesBeta

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

Checks run against github.com/kharchenkolab/pagoda2 on 2026-10-11.

Continuous integration (2)

Travis CI (config file)CircleCI

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

45 external dependencies (excludes base and recommended)

Installing pagoda2 adds 58 packages (36 with compiled code, 47 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, igraph 4.8 MB.

Depends (3)

R >= 3.5.0Matrixigraph

Imports (25)

dendsort drat fastclustergraphicsgrDevicesirlba magrittrMASSmgcvmethodsN2Rparallelplyr R.utils Rcpp rjson rlang R6 RMTstat Rook Rtsne sccore (>= 0.1.1)statsurltoolsutils

LinkingTo (4)

Rcpp RcppArmadillo RcppProgress RcppEigen

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

conos

Suggests, most downloaded first

CRMetrics lstar

How these are counted

Code & Tests

Datasets

People & History

People (6)

Evan Biederstedt

Maintainer since 1.0.0 (2021), Author

Author

Author

Author

Contributor · added in 1.0.11

Simon Steiger

Contributor

Releases (16)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-04-01
1.0.15Latest
record
2026-03-31 · current release · diff ↗
archivedRemoved from CRAN
2026-03-13
requires archived package 'N2R'
1.0.14
record
2026-03-08 · diff ↗
1.0.13
record
2025-08-18 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.12
record
2024-02-27 · diff ↗
1.0.11
record
2023-08-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.0.10
record
2022-04-19 · diff ↗
1.0.9
record
2022-03-02 · diff ↗
1.0.8
record
2021-12-12 · diff ↗
1.0.7
record
2021-11-15 · diff ↗

Show 9 earlier eventsHide 9 earlier events

1.0.6
record
2021-10-06 · diff ↗
1.0.5
record
2021-08-11 · diff ↗
1.0.4
record
2021-06-29 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.3
record
2021-05-04 · diff ↗
1.0.2
record
2021-03-04 · diff ↗
1.0.1
record
2021-02-23 · diff ↗
1.0.0
record
2021-01-28
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-01-28
Total releases: 16 / 5 yrs
License: GPL-3 OSI
Copyright: See the file COPYRIGHTS for various pagoda2 copyright details
Minimum R: ≥ 3.5.0
Download size: 533 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pagoda2")

Format

Biederstedt, E., Barkas, N., Kharchenko, P., Petukhov, V., Rydbirk, R., & Steiger, S. (2026). pagoda2: Single Cell Analysis and Differential Expression (Version 1.0.15) [Computer software]. https://doi.org/10.32614/CRAN.package.pagoda2

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 pagoda2 version 1.0.15 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →