Type: Package
Package: gimap
Title: Calculate Genetic Interactions for Paired CRISPR Targets
Version: 1.1.3
Authors@R: c(
  person("Candace", "Savonen",
         email = c("cansav09@gmail.com","csavonen@fredhutch.org"),
         role = c("aut", "cre"),
         comment = c(ORCID = "0000-0001-6331-7070")),
  person("Phoebe C.R.", "Parrish",
         email = "pcrparrish@gmail.com", role = c("aut"),
         comment = c(ORCID = "0000-0002-3530-0105")),
  person("Kathryn J.", "Isaac",
         email = "kisaac@fredhutch.org", role = c("aut"),
         comment = c(ORCID = "0000-0001-8701-4197")),
  person("Daniel", "Groso", role = c("aut")),
  person("Marissa", "Fujimoto", role = c("aut")),
  person("Siobhan", "O'Brien", role = c("aut"),
         comment = c(ORCID = "0000-0003-4958-1080")),
  person("Alice H.", "Berger", role = c("aut"),
         comment = c(ORCID = "0000-0002-6538-2658")))
Description: 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>.
License: BSD_3_clause + file LICENSE
URL: https://github.com/FredHutch/gimap
BugReports: https://github.com/FredHutch/gimap/issues
Depends: R (>= 3.5.0)
Imports: readr, dplyr, tidyr, rmarkdown, vroom, ggplot2, magrittr,
        pheatmap, purrr, janitor, utils, stats, stringr, httr,
        jsonlite, openssl
Suggests: testthat (>= 3.0.0), roxygen2, kableExtra, knitr
Config/testthat/edition: 3
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
        libx11-dev
Repository: https://fredhutch.r-universe.dev
Date/Publication: 2026-07-01 00:40:28 UTC
RemoteUrl: https://github.com/fredhutch/gimap
RemoteRef: HEAD
RemoteSha: 86ba77e553c98524712e3a0985a423e9b0296748
NeedsCompilation: no
Packaged: 2026-07-01 06:50:15 UTC; root
Author: Candace Savonen [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-6331-7070>),
  Phoebe C.R. Parrish [aut] (ORCID:
    <https://orcid.org/0000-0002-3530-0105>),
  Kathryn J. Isaac [aut] (ORCID: <https://orcid.org/0000-0001-8701-4197>),
  Daniel Groso [aut],
  Marissa Fujimoto [aut],
  Siobhan O'Brien [aut] (ORCID: <https://orcid.org/0000-0003-4958-1080>),
  Alice H. Berger [aut] (ORCID: <https://orcid.org/0000-0002-6538-2658>)
Maintainer: Candace Savonen <cansav09@gmail.com>