R Observatory: Metrics for topr version 2.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

topr

2.0.4Package record

Create Custom Plots for Viewing Genetic Association Results

0packages depend

8.5Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Thorhildur JuliusdottirCRAN page ↗GitHub ↗Issues ↗

A collection of functions for visualizing,exploring and annotating genetic association results.Association results from multiple traits can be viewed simultaneously along with gene annotation, over the entire genome (Manhattan plot) or in the more detailed regional view.

Changes in 2.0.4

Fixed an issue in foresttopr() where the first y-axis label could be clipped or not displayed.

From NEWS.md in the release

Install

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

install.packages("topr", 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("totajuliusd/topr")

Development version from totajuliusd/topr. 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-topr

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-topr

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-topr

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: 2.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-19
NOTE3 OK, 11 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.4

README· In the repository, left out of the releaseVignettes· In the repository, left out of the releaseNEWSYes · 100% structured · mentions 2.0.4Citation fileNo

The repository also keeps web-only articles.

Help pages: 37 (4 internal)includes a package overview page
Examples that run: 7%2 run in a plain check · 28 never run
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 97%
Help pages citing references: 0%

How these are measured

Downloads

8.5K

CRAN downloads in the past year

Rank #5,131 · ~23/day · ~711/mo

Releases R versions

Daily download trend is not available in this view yet.

54230 days

1.6K90 days

8.5K1 year

Compare downloads with other packages →

Also on102 r2u7 autocran

How downloads are counted

Repository

totajuliusd/topr ↗Account: totajuliusd

76Stars

16Forks

9Open issues

0Open PRs

17Releases

242Commits

14Commit identities

242 commits · Last activity 2026-04-26 · +1.3% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 98%
Median days to close, 50 most recently updated closed issues: 13
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-27 · 682026-09-29 · 76

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/totajuliusd/topr on 2026-10-18.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-04-26

Reproducibility and dev environment (1)

Makefile

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing topr adds 34 packages (17 with compiled code, 38 MB of source tarballs). Heaviest: stringi 11 MB, enshuman 6.6 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1.0

Imports (13)

ggplot2 dplyr stringr scales ggrepel egg gridExtra magrittrutilstidyr enshuman purrr tibble

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown markdown

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 (3)

Thorhildur Juliusdottir

Copyright holder, Author, Maintainer since 1.0.0 (2022)

Andri Stefansson

Author

Kyle Scott

Contributor · added in 2.0.3

Listed in earlier versions (1)

Genuity Science

no longer listed · 1.0.0 to 1.1.2

Releases (17)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.0.4Latest
record
2026-04-13 · current release · diff ↗
2.0.3
record
2026-04-12 · diff ↗ ·
added 2 exports
foresttopr, get_topr_old_colors
R
R 4.5.0 released · 2025-04-11
2.0.2
record
2024-06-19 · diff ↗ ·
added 2 exports
get_sign_and_sugg_loci, manhattanExtra
R
R 4.4.0 released · 2024-04-24
2.0.1
record
2024-03-15 · diff ↗
2.0.0
record
2024-02-04 · diff ↗
1.1.10
record
2023-09-13 · diff ↗
1.1.9
record
2023-09-06 · diff ↗
1.1.8
record
2023-08-26 · diff ↗
1.1.7
record
2023-05-23 · diff ↗
1.1.6
record
2023-04-26 · diff ↗
1.1.5
record
2023-04-25 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.4
record
2023-03-09 · diff ↗

Show 7 earlier eventsHide 7 earlier events

1.1.3
record
2023-02-12 · diff ↗
1.1.2
record
2023-01-13 · diff ↗
1.1.1
record
2022-11-04 · diff ↗
1.1.0
record
2022-10-25 · diff ↗ ·
added 8 exports
effectplot, get_gene_coords, get_genes_in_region, get_lead_snps, get_snpset, get_snpset_code, match_by_alleles, match_by_pos
R
R 4.2.0 released · 2022-04-22
1.0.0
record
2022-01-12
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-12
Total releases: 17 / 4 yrs
License: LGPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.9 MB / 4 files
Download size: 2.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("topr")

Format

Juliusdottir, T., Scott, K., & Stefansson, A. (2026). topr: Create Custom Plots for Viewing Genetic Association Results (Version 2.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.topr

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 topr version 2.0.4 [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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