isatabr

1.0.1

Implementation for the ISA Abstract Model

0packages depend

2.7Kdownloads / year

82.4%test coverage

13/13checks pass

Overview

About

Maintained by Bart-Jan van RossumFirst published 2021-07-162 releasesCRAN page ↗GitHub ↗

ISA is a metadata framework to manage an increasingly diverse set of life science, environmental and biomedical experiments. In isatabr methods for reading, modifying and writing of files in the ISA-Tab format are implemented. It also contains methods for processing assay data.

Install

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

install.packages("isatabr", 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("Biometris/isatabr")

Development version from Biometris/isatabr. 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-isatabr

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-isatabr

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-isatabr

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

Health

CRAN checks

13OK

Slowest check: 2.9 min · r-devel-linux-x86_64-fedora-gcc

Code health

Yes

Tests · ratio 0.00

82.4%

Coverage · measured lines

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-06-08
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

2.7K

CRAN downloads in the past year

Rank #16,109 · ~7/day · ~223/mo

Releases R versions

Daily download trend is not available in this view yet.

25230 days

70090 days

2.7K1 year

Compare downloads with other packages →

Also on110 r2u17 autocran

Repository

GitHub ↗ biometris/isatabr

0Stars

0Forks

0Open issues

0Open PRs

0Releases

cranisaisatabr-package

Last activity 2023-08-25

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

methods

Imports (0)

none

LinkingTo (0)

none

Suggests (6)

tinytest affy Biobase xcms knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 2,051 (59%)Rd 1,129 (32%)Vignettes 290 (8%)Other 26 (1%)

Code characteristics

Object systems

S4 class4S4 generic31S4 method34

Cyclomatic complexity: 2.5 median / 5 max
Test cases: 83 / 0.00 per code line
Documented parameters: 99%

Test coverage

Line coverage

82%

Expression

83.7%

Tests / Examples

82.4% / 66% ex

Functions

18 9 exported

Complexity

2.4 avg / 5 max

Call network

18 nodes / 14 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

18 functions

Function	Cyclo	Coverage
constructMIAMEMetadata	3	0%
getFactors	1	0%
getAssayFileNames exp	1	100%
getAssayTabs exp	2	100%
getStudyFileNames exp	1	100%
readISATab exp	3	100%

People & History

People (2)

Maintainer (1)

Bart-Jan van Rossum

Author, Maintainer

Authors (2)

Bart-Jan van Rossum

Author, Maintainer

Maikel Verouden

Author

Package Timeline

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

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
1.0.1Latest
2022-08-19 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.0
2021-07-16
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-16
Total releases: 2 / 5 yrs
License: GPL-3 OSI
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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