Package: SpatialDDLS
Type: Package
Title: Deconvolution of Spatial Transcriptomics Data Based on Neural
        Networks
Version: 1.0.3
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 based on neural networks and single-cell RNA-seq data. SpatialDDLS implements a workflow to create neural network models able to make accurate estimates of cell composition of spots from spatial transcriptomics data using 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. (2024) <doi:10.1093/bioinformatics/btae072> 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: 7.3.2
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: 2024-10-31 08:55:20 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: 2024-10-31 09:40:06 UTC
Built: R 4.4.3; ; 2025-11-12 05:56:15 UTC; windows
