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.

Author
Ting Gong <tinggong@gmail.com> Joseph D. Szustakowski <joseph.szustakowski@novartis.com>
Date of publication
None
Maintainer
Ting Gong <tinggong@gmail.com>
License
GPL-2
Version
1.16.0

View on Bioconductor

Man pages

all.datasets
data objects for rat liver_brain samples
array.proportions
proportions for rat liver and brain mixing samples
array.signatures
data objects for rat liver and brain pure samples
condplot
Draw the plot of the condition numbers vs. the number of...
datasets
data objects for liver and kidney mixing samples
decon.bootstrap
Estimate the confidence interval for the proportions...
DeconRNASeq
Function for Deconvolution of Complex Samples from RNA-Seq.
DeconRNASeq-package
package DeconRNASeq contains function "DeconRNASeq",...
fraction
mixing fractions for multi-tissues mixing samples
liver_kidney
data objects for liver and kidney mixing samples
multiplot
Draw the plots of proportions of cells determined from...
multi_tissue
data objects for multi-tissues mixing samples
proportions
proportions for liver and kidney mixing samples
rmse
Calculate the differences between proportions predicted by...
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

Files in this package

DeconRNASeq/.BBSoptions
DeconRNASeq/DESCRIPTION
DeconRNASeq/NAMESPACE
DeconRNASeq/R
DeconRNASeq/R/DeconRNASeq.R
DeconRNASeq/R/decon.bootstrap.R
DeconRNASeq/R/multiplot.R
DeconRNASeq/R/rmse.R
DeconRNASeq/build
DeconRNASeq/build/vignette.rds
DeconRNASeq/data
DeconRNASeq/data/datalist
DeconRNASeq/data/liver_kidney.rda
DeconRNASeq/data/liver_kidney_ascii.rda
DeconRNASeq/data/multi_tissue.rda
DeconRNASeq/data/rat_liver_brain.rda
DeconRNASeq/demo
DeconRNASeq/demo/00Index
DeconRNASeq/demo/DeconRNASeq.R
DeconRNASeq/inst
DeconRNASeq/inst/doc
DeconRNASeq/inst/doc/DeconRNASeq.R
DeconRNASeq/inst/doc/DeconRNASeq.Rnw
DeconRNASeq/inst/doc/DeconRNASeq.pdf
DeconRNASeq/man
DeconRNASeq/man/DeconRNASeq-package.Rd
DeconRNASeq/man/DeconRNASeq.Rd
DeconRNASeq/man/all.datasets.Rd
DeconRNASeq/man/array.proportions.Rd
DeconRNASeq/man/array.signatures.Rd
DeconRNASeq/man/condplot.Rd
DeconRNASeq/man/datasets.Rd
DeconRNASeq/man/decon.bootstrap.Rd
DeconRNASeq/man/fraction.Rd
DeconRNASeq/man/liver_kidney.Rd
DeconRNASeq/man/multi_tissue.Rd
DeconRNASeq/man/multiplot.Rd
DeconRNASeq/man/proportions.Rd
DeconRNASeq/man/rmse.Rd
DeconRNASeq/man/signatures.Rd
DeconRNASeq/man/x.data.Rd
DeconRNASeq/man/x.signature.Rd
DeconRNASeq/man/x.signature.filtered.Rd
DeconRNASeq/man/x.signature.filtered.optimal.Rd
DeconRNASeq/vignettes
DeconRNASeq/vignettes/DeconRNASeq.Rnw