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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.
Version: | 1.0.1 |
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 |
Published: | 2024-02-07 |
Author: | Diego Mañanes [aut, cre], Carlos Torroja [aut], Fatima Sanchez-Cabo [aut] |
Maintainer: | Diego Mañanes <dmananesc at cnic.es> |
BugReports: | https://github.com/diegommcc/digitalDLSorteR/issues |
License: | GPL-3 |
URL: | https://diegommcc.github.io/digitalDLSorteR/, https://github.com/diegommcc/digitalDLSorteR |
NeedsCompilation: | no |
SystemRequirements: | Python (>= 2.7.0), TensorFlow (https://www.tensorflow.org/) |
Citation: | digitalDLSorteR citation info |
Materials: | README NEWS |
CRAN checks: | digitalDLSorteR results |
Reference manual: | digitalDLSorteR.pdf |
Vignettes: |
Building new deconvolution models |
Package source: | digitalDLSorteR_1.0.1.tar.gz |
Windows binaries: | r-devel: digitalDLSorteR_1.0.1.zip, r-release: digitalDLSorteR_1.0.1.zip, r-oldrel: digitalDLSorteR_1.0.1.zip |
macOS binaries: | r-release (arm64): digitalDLSorteR_1.0.1.tgz, r-oldrel (arm64): digitalDLSorteR_1.0.1.tgz, r-release (x86_64): digitalDLSorteR_1.0.1.tgz, r-oldrel (x86_64): digitalDLSorteR_1.0.1.tgz |
Old sources: | digitalDLSorteR archive |
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