R Observatory: Metrics for GenomicTools.fileHandler version 0.1.5.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GenomicTools.fileHandler

0.1.5.9Package record

File Handlers for Genomic Data Analysis

0packages depend

4.2Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Daniel FischerCRAN page ↗

A collection of I/O tools for handling the most commonly used genomic datafiles, like fasta/-q, bed, gff, gtf, ped/map and vcf.

Install

R (CRAN)Ubuntu (r2u)

install.packages("GenomicTools.fileHandler", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-genomictools.filehandler

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

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Daniel Fischer <daniel.fischer@luke.fi>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Daniel",
                    family = "Fischer",
                    role = c("aut", "cre"),
                    email = "daniel.fischer@luke.fi")
as necessary.

CRAN check page ↗

Slowest check: 2.9 min · r-release-macos-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.5.9

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 39includes a package overview page
Examples that run: 100%10 run in a plain check
Exported functions with examples: 63%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

An Introduction to GenomicTools.fileHandler

How these are measured

Downloads

4.2K

CRAN downloads in the past year

Rank #12,272 · ~11/day · ~348/mo

Releases R versions

Daily download trend is not available in this view yet.

30730 days

90490 days

4.2K1 year

Compare downloads with other packages →

Also on89 r2u385 bioconda25 c2d4u

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing GenomicTools.fileHandler adds 1 package (1 with compiled code, 5.7 MB of source tarballs). Heaviest: data.table 5.7 MB. 1 more not on CRAN is not measured.

Depends (2)

R >= 3.3data.table

Imports (1)

snpStats

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (1)

Daniel Fischer

Maintainer since 0.1.2 (2018)

Releases (4)

Pick two releases to compare their code metrics.

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
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.5.9Latest
record
2020-03-05 · current release · diff ↗
0.1.5.8
record
2020-02-11 · diff ↗ ·
added 2 exports
plotTotalReads, plotUniquelyMappedReads
R
R 3.6.0 released · 2019-04-26
0.1.4
record
2019-02-06 · diff ↗
0.1.2
record
2018-08-16
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-08-16
Total releases: 4 / 8 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.3
Download size: 558 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("GenomicTools.fileHandler")

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 GenomicTools.fileHandler version 0.1.5.9 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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