geneHummus

1.0.11

A Pipeline to Define Gene Families in Legumes and Beyond

0packages depend

2.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Jose V. DieFirst published 2019-03-253 releasesCRAN page ↗GitHub ↗

A pipeline with high specificity and sensitivity in extracting proteins from the RefSeq database (National Center for Biotechnology Information). Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family. The pipelines implements an automatic approach for the identification of gene families based on the conserved domains that specifically define that family. See Die et al. (2018) doi:10.1101/436659 for more information and examples.

Install

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

install.packages("geneHummus", 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("NCBI-Hackathons/GeneHummus")

Development version from NCBI-Hackathons/GeneHummus. 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-genehummus

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-geneHummus

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-geneHummus

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

Health

CRAN checks

13OK

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-05-11
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-10
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 150 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.6K

CRAN downloads in the past year

Rank #19,033 · ~7/day · ~214/mo

Releases R versions

Daily download trend is not available in this view yet.

21830 days

59290 days

2.6K1 year

Compare downloads with other packages →

Also on97 r2u2 autocran

Repository

GitHub ↗ ncbi-hackathons/genehummus

8Stars

2Forks

0Open issues

0Open PRs

3Releases

197Commits

5Contributors

197 commits · Last activity 2020-09-02

Stars over time

2025-03-11 · 82026-07-07 · 8

Repository practices

Upstream repositoryBeta

Checks run against github.com/ncbi-hackathons/genehummus on 2026-07-30.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (6)

rentrez stringr dplyr httrutilscurl

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Jose V. Die

Author, Maintainer

Authors (2)

Jose V. Die

Author, Maintainer

Ben Busby

Author

Contributors (4)

Contributor

Contributor

Contributor

Contributor

Package Timeline

3 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
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
R
R 3.6.0 released · 2019-04-26
1.0.11Latest
2019-04-05 · current release · diff ↗
1.0.1
2019-03-26 · diff ↗
unarchivedReturned to CRAN
2019-03-26
1.0.0
2019-03-25
archivedRemoved from CRAN
2019-03-25
policy violation Internet access is not guarded
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-03-25
Total releases: 3 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.4.0
Bundled data: 25 KB / 2 files
Download size: 60 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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