Package: DeconRNASeq 1.54.0

Ting Gong

DeconRNASeq: Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data

DeconSeq is an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.

Authors:Ting Gong <[email protected]> Joseph D. Szustakowski <[email protected]>

DeconRNASeq_1.54.0.tar.gz
DeconRNASeq_1.54.0.zip(r-4.7)DeconRNASeq_1.54.0.zip(r-4.6)DeconRNASeq_1.54.0.zip(r-4.5)
DeconRNASeq_1.54.0.tgz(r-4.6-any)DeconRNASeq_1.54.0.tgz(r-4.5-any)
DeconRNASeq_1.54.0.tar.gz(r-4.7-any)DeconRNASeq_1.54.0.tar.gz(r-4.6-any)
DeconRNASeq_1.54.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DeconRNASeq/json (API)

# Install 'DeconRNASeq' in R:
install.packages('DeconRNASeq', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • datasets - Data objects for liver and kidney mixing samples
  • datasets - Data objects for liver and kidney mixing samples
  • fraction - Mixing fractions for multi-tissues mixing samples
  • proportions - Proportions for liver and kidney mixing samples
  • proportions - Proportions for liver and kidney mixing samples
  • signatures - Data objects for liver and kidney pure samples
  • signatures - Data objects for liver and kidney pure samples
  • x.data - Data objects for multi-tissues mixing samples
  • x.signature - Data objects for multi-tissues pure samples
  • x.signature.filtered - Filtered signatures for multi-tissues pure samples
  • x.signature.filtered.optimal - Selected signatures from multi-tissues pure samples

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

differentialexpression

3.43 score 89 scripts 790 downloads 23 mentions 5 exports 26 dependencies

Last updated from:473698cc2b (on RELEASE_3_23). Checks:1 FAILURE, 7 WARNING, 1 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksFAILURE137
linux-devel-x86_64WARNING131
source / vignettesERROR164
linux-release-x86_64WARNING144
macos-release-arm64WARNING99
macos-oldrel-arm64WARNING105
windows-develWARNING83
windows-releaseWARNING72
windows-oldrelWARNING82
wasm-releaseOK102

Exports:condplotdecon.bootstrapDeconRNASeqmultiplotrmse

Dependencies:BiobaseBiocGenericsclicpp11farvergenericsggplot2gluegtableisobandlabelinglifecyclelimSolvelpSolveMASSpcaMethodsquadprogR6RColorBrewerRcpprlangS7scalesvctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
package DeconRNASeq contains function "DeconRNASeq", implementing the decomposition of RNA-Seq expression profilings of heterogeneous tissues into cell/tissue type specific expression and cell type concentration based on cell-type-specific reference measurements.DeconRNASeq.package DeconRNASeq_package
data objects for rat liver_brain samplesall.datasets
proportions for rat liver and brain mixing samplesarray.proportions
data objects for rat liver and brain pure samplesarray.signatures
Draw the plot of the condition numbers vs. the number of genes in the signature matrixcondplot
data objects for liver and kidney mixing samplesdatasets
Estimate the confidence interval for the proportions predicted by deconvolutiondecon.bootstrap
Function for Deconvolution of Complex Samples from RNA-Seq.DeconRNASeq
mixing fractions for multi-tissues mixing samplesfraction
data objects for liver and kidney mixing samplesliver_kidney
data objects for multi-tissues mixing samplesmulti_tissue
Draw the plots of proportions of cells determined from deconvolution vs. proportions of the cells actually mixed (when available) with RMSE.multiplot
proportions for liver and kidney mixing samplesproportions
Calculate the differences between proportions predicted by deconvolution and the values actually measuredrmse
data objects for liver and kidney pure samplessignatures
data objects for multi-tissues mixing samplesx.data
data objects for multi-tissues pure samplesx.signature
filtered signatures for multi-tissues pure samplesx.signature.filtered
selected signatures from multi-tissues pure samplesx.signature.filtered.optimal