R Observatory: Metrics for gimap version 1.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

gimap

1.1.3Package record

Calculate Genetic Interactions for Paired CRISPR Targets

0packages depend

5.7Kdownloads / year

64.7%test coverage

13/13flavors OK

Overview

About

Maintained by Candace SavonenCRAN page ↗GitHub ↗Issues ↗

Helps find meaningful patterns in complex genetic experiments. First gimap takes data from paired CRISPR (Clustered regularly interspaced short palindromic repeats) screens that has been pre-processed to counts table of paired gRNA (guide Ribonucleic Acid) reads. The input data will have cell counts for how well cells grow (or don't grow) when different genes or pairs of genes are disabled. The output of the 'gimap' package is genetic interaction scores which are the distance between the observed CRISPR score and the expected CRISPR score. The expected CRISPR scores are what we expect for the CRISPR values to be for two unrelated genes. The further away an observed CRISPR score is from its expected score the more we suspect genetic interaction. The work in this package is based off of original research from the Alice Berger lab at Fred Hutchinson Cancer Center (2021) doi:10.1016/j.celrep.2021.109597.

Changes in 1.1.3

Updated package metadata for the JOSS software release.
Added ORCIDs and aligned package citation metadata with the JOSS paper.
Declared the BSD 3-Clause license using CRAN's standard license expression.

From NEWS.md in the release

Install

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

install.packages("gimap", 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("FredHutch/gimap")

Development version from FredHutch/gimap. 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-gimap

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-gimap

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-gimap

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 OK2026-10-20
ERROR12 OK, 1 ERROR2026-10-17
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 3 earlier changesHide 3 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.3

READMEYes · 1,942 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 1.1.3Citation fileYes · software entry only

Help pages: 41 (6 internal)
Examples that run: 8%2 run in a plain check · 22 never run
Exported functions with examples: 80%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

5.7K

CRAN downloads in the past year

Rank #8,107 · ~16/day · ~472/mo

Releases R versions

Daily download trend is not available in this view yet.

47130 days

1.1K90 days

5.7K1 year

Compare downloads with other packages →

Also on114 r2u4 autocran

How downloads are counted

Repository

fredhutch/gimap ↗Organization: FredHutch

1Stars

4Forks

8Open issues

0Open PRs

2Releases

716Commits

9Commit identities

716 commits · Last activity 2026-07-31 · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 96%
Median days to close, 50 most recently updated closed issues: 101
Median days to close, 50 most recently updated closed PRs: 6

Stars over time

2025-07-25 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/fredhutch/gimap on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (5)

Code of conductContributing guideIssue templatesPR templateSecurity policy

Docs source (1)

GitHub Pages site last deployed 2026-07-31

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 2 practices

Research and citation (2)

JOSS paperZenodo

Lint, format, editor (2)

Lint workflowRStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Cursorfirst seen 2026-06-29
Commits: at least 3 crediting it in the message

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing gimap adds 70 packages (38 with compiled code, 50 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (1)

R >= 3.5.0

Imports (16)

readr dplyr tidyr rmarkdown vroom ggplot2 magrittr pheatmap purrr janitorutilsstatsstringr httr jsonlite openssl

LinkingTo (0)

none

Suggests (4)

testthat roxygen2 kableExtra knitr

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 (7)

Candace Savonen

Author, Maintainer since 1.0.1 (2025)

Alice H. Berger

Author · added in 1.1.3

Marissa Fujimoto

Author · added in 1.1.1

Daniel Groso

Author · added in 1.1.3

Kathryn J. Isaac

Author · added in 1.1.3

Siobhan O'Brien

Author

Phoebe C.R. Parrish

Author · added in 1.1.3

Listed in earlier versions (5)

Show 5 peopleHide 5 people

Howard Baek