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DESCRIPTION
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DESCRIPTION
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Package: digitalDLSorteR
Type: Package
Title: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
Version: 1.1.1
Authors@R: c(
person(given = "Diego", family = "Mañanes", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7247-6794")),
person(given = "Carlos", family = "Torroja", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0001-8914-3400")),
person(given = "Fatima", family = "Sanchez-Cabo", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0003-1881-1664")))
Maintainer: Diego Mañanes <[email protected]>
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,
ComplexHeatmap,
testthat
SystemRequirements: Python (>= 2.7.0), TensorFlow (https://www.tensorflow.org/)
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
Collate:
'AllClasses.R'
'AllGenerics.R'
'digitalDLSorteR.R'
'dnnModel.R'
'evalMetrics.R'
'interGradientsDL.R'
'loadData.R'
'simBulk.R'
'simSingleCell.R'
'utils.R'
VignetteBuilder: knitr