R Observatory: Metrics for inDAGO version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

inDAGO

1.0.4Package record

A GUI for Dual and Bulk RNA-Sequencing Analysis

0packages depend

3Kdownloads / year

0.1%test coverage

13/13flavors OK

Overview

About

Maintained by Carmine FruggieroCRAN page ↗GitHub ↗Website ↗Issues ↗

A 'shiny' app that supports both dual and bulk RNA-seq, with the dual RNA-seq functionality offering the flexibility to perform either a sequential approach (where reads are mapped separately to each genome) or a combined approach (where reads are aligned to a single merged genome). The user-friendly interface automates the analysis process, providing step-by-step guidance, making it easy for users to navigate between different analysis steps, and download intermediate results and publication-ready plots.

Install

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

install.packages("inDAGO", 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("inDAGOverse/inDAGO")

Development version from inDAGOverse/inDAGO. 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-indago

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-inDAGO

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-inDAGO

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: 7.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-23
ERROR12 OK, 1 ERROR2026-08-22
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 3 earlier changesHide 3 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.4

READMENoVignettesNoNEWSNoCitation fileNoWebsiteYes

Help pages: 66
Examples that run: no examples
Exported functions with examples: 0%
Documented parameters: not tracked
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #12,110 · ~8/day · ~248/mo

Releases R versions

Daily download trend is not available in this view yet.

31730 days

91090 days

3K1 year

Compare downloads with other packages →

Also on75 r2u4 autocran

How downloads are counted

Repository

indagoverse/indago ↗Organization: inDAGOverse

3Stars

1Forks

0Open issues

0Open PRs

3Releases

185Commits

1Commit identities

License file reads as GPL-3.0 · 185 commits · Last activity 2026-08-13 · 0% stars, 30d · The default branch showed an older version (1.0.3) than CRAN on 2026-10-22

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 61
Median days to close, 50 most recently updated closed PRs: 57

Stars over time

2025-06-15 · 12026-07-07 · 3

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/indagoverse/indago on 2026-10-22.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

51 external dependencies (excludes base and recommended)

Installing inDAGO adds 138 packages (64 with compiled code, 122 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (0)

none

Imports (41)

bsicons bslib callr checkmate data.table dplyr DT fs ggplot2 ggrepelgrDevicesheatmaply Hmisc htmltools magrittr matrixStats memusemethodspaletteerparallelpheatmap plotly R.devices readr reshape2 rintrojs seqinr shiny shinycssloaders shinyFiles shinyjs shinyWidgets spsCompsstatssvglite tibble tidyrtoolsupsetjs UpSetRutils

LinkingTo (0)

none

Suggests (16)

BiocGenerics BiocManager Biostrings edgeR harrypotter HTSFilter limma oompaBase palr Rsamtools Rsubread rtracklayer S4Vectors ShortRead testthat XVector

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Carmine Fruggiero

Author, Maintainer since 1.0.0 (2025)

Gaetano Aufiero

Author

Releases (5)

Pick two releases to compare their code metrics.

1.0.4Latest
record
2026-08-21 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.3
record
2025-10-21 · diff ↗
1.0.2
record
2025-09-19 · diff ↗
1.0.1
record
2025-09-13 · diff ↗
1.0.0
record
2025-07-05
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-07-05
Total releases: 5 / 1 yrs
License: GPL (>= 3) OSI
Download size: 441 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("inDAGO")

Format

Fruggiero, C., & Aufiero, G. (2026). inDAGO: A GUI for Dual and Bulk RNA-Sequencing Analysis (Version 1.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.inDAGO

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 inDAGO version 1.0.4 [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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