Package: STACAS
Type: Package
Title: STACAS: Sub-Type Anchoring Correction for Alignment in Seurat
Version: 2.4.1
Authors@R: c(
  person(given = 'Massimo', family = 'Andreatta', email = 'massimo.andreatta@unil.ch', role = c('aut','cre'), comment = c(ORCID = '0000-0002-8036-2647')),
  person(given = 'Ariel', family = 'Berenstein', email = 'arieljberenstein@gmail.com', role = c('aut'), comment = c(ORCID = '0000-0001-8540-5389')),
  person(given = 'Josep', family = 'Garnica', email = 'Josep.Garnicacaparros@unige.ch', role = c('aut'), comment = c(ORCID = '0000-0001-9493-1321')),
  person(given = 'Santiago', family = 'Carmona', email = 'santiago.carmona@unil.ch', role = c('aut'), comment = c(ORCID = '0000-0002-2495-0671'))
  )
Description: This package implements methods for batch correction and
        integration of scRNA-seq datasets, based on the popular Seurat
        anchor-based integration framework. In particular, STACAS is
        optimized for the integration of heterogenous datasets with
        only limited overlap between cell sub-types (e.g. TIL sets of
        CD8 from tumor with CD8/CD4 T cells from lymphnode), for which
        the default Seurat alignment methods would tend to over-correct
        biological differences. The 2.0 version of our package allows
        to the users to incorporate explicit information about
        cell-types in order to assist the integration process.
biocViews:
Depends: R (>= 4.0.0)
Imports: Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), data.table, pbapply,
        ggridges, colorspace, R.utils, ggplot2, stats, BiocNeighbors,
        BiocParallel
Suggests: testthat (>= 3.0.0), sf
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.2
Config/testthat/edition: 3
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://carmonalab.r-universe.dev
Date/Publication: 2026-01-27 09:46:28 UTC
RemoteUrl: https://github.com/carmonalab/STACAS
RemoteRef: HEAD
RemoteSha: ea34e824e17df6316823db0a9b6322af0833e501
NeedsCompilation: no
Packaged: 2026-05-27 06:44:53 UTC; root
Author: Massimo Andreatta [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-8036-2647>),
  Ariel Berenstein [aut] (ORCID: <https://orcid.org/0000-0001-8540-5389>),
  Josep Garnica [aut] (ORCID: <https://orcid.org/0000-0001-9493-1321>),
  Santiago Carmona [aut] (ORCID: <https://orcid.org/0000-0002-2495-0671>)
Maintainer: Massimo Andreatta <massimo.andreatta@unil.ch>