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DESCRIPTION
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DESCRIPTION
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Package: STACAS
Type: Package
Title: STACAS: Sub-Type Anchoring Correction for Alignment in Seurat
Version: 2.2.2
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 = '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(>= 4.0.0),
pbapply,
ggridges,
R.utils,
ggplot2,
stats,
BiocNeighbors,
BiocParallel
Suggests: sf
License: GPL-3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.1