R Observatory: Metrics for Map2NCBI version 1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Map2NCBI

1.5Package record

Mapping Markers to the Nearest Genomic Feature

0packages depend

6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Lauren L. Hulsman HannaCRAN page ↗

Allows the user to generate a list of features (gene, pseudo, RNA, CDS, and/or UTR) directly from NCBI database for any species with a current build available. Option to save downloaded and formatted files is available, and the user can prioritize the feature list based on type and assembly builds present in the current build used. The user can then use the list of features generated or provide a list to map a set of markers (designed for SNP markers with a single base pair position available) to the closest feature based on the map build. This function does require map positions of the markers to be provided and the positions should be based on the build being queried through NCBI.

Install

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

install.packages("Map2NCBI", 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-map2ncbi

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-Map2NCBI

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-Map2NCBI

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: 57 s · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.5

READMENoVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 5includes a package overview page
Examples that run: 60%3 run in a plain check · 1 never run · 1 hold no code
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 80%

How these are measured

Downloads

6K

CRAN downloads in the past year

Rank #10,247 · ~17/day · ~502/mo

Releases R versions

Daily download trend is not available in this view yet.

38330 days

98790 days

6K1 year

Compare downloads with other packages →

Also on84 r2u2 autocran44 c2d4u

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing Map2NCBI adds 10 packages (7 with compiled code, 4.0 MB of source tarballs). Heaviest: openssl 1.1 MB, jsonlite 1.0 MB, XML 937 KB.

Depends (2)

R >= 3.5rentrez

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

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 (2)

Lauren L. Hulsman Hanna

Author, Maintainer since 1.0 (2013)

David G. Riley

Author

Listed in earlier versions (2)

David G.

no longer listed · 1.5

Lauren L.

no longer listed · 1.5

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.5Latest
record
2025-04-18 · current release · diff ↗
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
1.4
record
2020-01-24 · diff ↗
1.3
record
2019-05-15 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.2
record
2019-04-17 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.1
record
2015-11-13 · diff ↗

Show 4 earlier eventsHide 4 earlier events

R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
1.0
record
2013-09-24
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-09-24
Total releases: 6 / 13 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5
Bundled data: 38 KB / 2 files
Download size: 50 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("Map2NCBI")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1016/j.livsci.2014.01.019.

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 Map2NCBI version 1.5 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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