Package: grasspio
Type: Package
Title: Exchange Spatial Proteomics Data Between pRoloc and grassp
Version: 0.1.0
Authors@R: person(given = "Max", family = "Frank",
                  email = "max.frank@czbiohub.org",
                  role = c("aut", "cre"))
Description: Converts between MSnbase 'MSnSet' objects, as used by the 'pRoloc'
             and 'bandle' spatial proteomics frameworks, and h5ad files, the
             format of the Python package 'grassp'. The two data models are
             nearly isomorphic -- both hold a features-by-fractions quantitation
             matrix with feature and sample metadata -- but they share no file
             format. This package supplies both directions, so an analysis can
             be preprocessed in one language, classified in the other, and
             brought back without losing annotations. There is no exchange
             format to keep in step: the files are ordinary h5ad, written and
             read on the Python side with 'anndata' itself. Matrix-valued
             feature metadata columns, which pRoloc uses for per-protein by
             per-compartment score matrices, are mapped onto AnnData's 'obsm' as
             data frames, so that they carry their own class names. Note that
             pRoloc has no exporter of its own, so 'grassp_write_msnset' is
             useful even without grassp.
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
Depends:
    R (>= 4.5)
Imports:
    anndataR (>= 1.3.1),
    Biobase,
    MSnbase,
    methods,
    utils
Suggests:
    rhdf5,
    pRoloc,
    testthat (>= 3.0.0),
    Matrix,
    knitr,
    rmarkdown
Remotes:
    github::mffrank/anndataR@fix-obsm-varm-data-frame-index
VignetteBuilder: knitr
URL: https://github.com/czbiohub-sf/grassp
BugReports: https://github.com/czbiohub-sf/grassp/issues
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
