Package: SpatialDDLS
Type: Package
Title: Deconvolution of Spatial Transcriptomics Data Based on Neural
        Networks
Version: 1.0.0
Authors@R: c(
  person(given = "Diego", family = "Mañanes", email = "dmananesc@cnic.es", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7247-6794")),
  person(given = "Carlos", family = "Torroja", email = "ctorroja@cnic.es", role = "aut", comment = c(ORCID = "0000-0001-8914-3400")),
  person(given = "Fatima", family = "Sanchez-Cabo", email = "fscabo@cnic.es", role = "aut", comment = c(ORCID = "0000-0003-1881-1664")))
Maintainer: Diego Mañanes <dmananesc@cnic.es>
Description: Deconvolution of spatial transcriptomics data using deconvolution models based on deep neural networks and single-cell RNA-seq data. These models are able to make accurate estimates of the cell composition of spots in spatial transcriptomics datasets from the same context using the advances provided by deep learning and the meaningful information provided by single-cell RNA-Seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> and Mañanes et al. (2023) <doi:10.1101/2023.08.31.555677> to get an overview of the method and see some examples of its performance. 
License: GPL-3
URL: https://diegommcc.github.io/SpatialDDLS/,
        https://github.com/diegommcc/SpatialDDLS
BugReports: https://github.com/diegommcc/SpatialDDLS/issues
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: rlang, grr, Matrix, methods, SpatialExperiment,
        SingleCellExperiment, SummarizedExperiment, zinbwave, stats,
        pbapply, S4Vectors, dplyr, reshape2, gtools, reticulate, keras,
        tensorflow, FNN, ggplot2, ggpubr, scran, scuttle
Suggests: knitr, rmarkdown, BiocParallel, rhdf5, DelayedArray,
        DelayedMatrixStats, HDF5Array, testthat, ComplexHeatmap, grid,
        bluster, lsa, irlba
SystemRequirements: Python (>= 2.7.0), TensorFlow
        (https://www.tensorflow.org/)
RoxygenNote: 7.2.3
Collate: 'AllClasses.R' 'AllGenerics.R' 'SpatialDDLS.R' 'dnnModel.R'
        'evalMetrics.R' 'interGradientsDL.R' 'loadData.R'
        'plotSpatialCoor.R' 'simMixedSpots.R' 'simSingleCell.R'
        'spatialClustering.R' 'utils.R'
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-12-06 08:56:37 UTC; dmananes
Author: Diego Mañanes [aut, cre] (<https://orcid.org/0000-0001-7247-6794>),
  Carlos Torroja [aut] (<https://orcid.org/0000-0001-8914-3400>),
  Fatima Sanchez-Cabo [aut] (<https://orcid.org/0000-0003-1881-1664>)
Repository: CRAN
Date/Publication: 2023-12-06 10:00:09 UTC
