Package: digitalDLSorteR
Type: Package
Title: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
Version: 1.0.1
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 bulk RNA-Seq data using context-specific deconvolution models based on Deep Neural Networks using scRNA-Seq data as input. These models are able to make accurate estimates of the cell composition of bulk RNA-Seq samples from the same context using the advances provided by Deep Learning and the meaningful information provided by scRNA-Seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> for more details.
License: GPL-3
URL: https://diegommcc.github.io/digitalDLSorteR/,
        https://github.com/diegommcc/digitalDLSorteR
BugReports: https://github.com/diegommcc/digitalDLSorteR/issues
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: rlang, grr, Matrix, methods, tidyr, SingleCellExperiment,
        SummarizedExperiment, zinbwave, stats, pbapply, S4Vectors,
        dplyr, tools, reshape2, gtools, reticulate, keras, tensorflow,
        ggplot2, ggpubr, scran, scuttle
Suggests: knitr, rmarkdown, BiocParallel, rhdf5, DelayedArray,
        DelayedMatrixStats, HDF5Array, testthat
SystemRequirements: Python (>= 2.7.0), TensorFlow
        (https://www.tensorflow.org/)
RoxygenNote: 7.2.3
Collate: 'AllClasses.R' 'AllGenerics.R' 'digitalDLSorteR.R'
        'dnnModel.R' 'evalMetrics.R' 'loadData.R' 'simBulk.R'
        'simSingleCell.R' 'utils.R'
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-02-07 09:41:54 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: 2024-02-07 10:30:02 UTC
Built: R 4.2.3; ; 2024-04-24 03:52:49 UTC; windows
