Table 1.

Summary of the tested deconvolution methods

MethodInputTypeAvailability
RodeoCexpressionR/Rodeo
cs-lsfitCexpressionR/CellMix
cs-qprogCexpressionR/CellMix
LRCDECexpressionR/LRCDE
csSAMCexpressionR/csSAM
DeblenderCcompleteMatlab
CDSeq#TcompleteMatlab, Octave, R
LinSeed#TcompleteR/linseed
Deconf#TcompleteR/CellMix
MethodInputTypeAvailability
RodeoCexpressionR/Rodeo
cs-lsfitCexpressionR/CellMix
cs-qprogCexpressionR/CellMix
LRCDECexpressionR/LRCDE
csSAMCexpressionR/csSAM
DeblenderCcompleteMatlab
CDSeq#TcompleteMatlab, Octave, R
LinSeed#TcompleteR/linseed
Deconf#TcompleteR/CellMix

Column ’Input’ describes required input data from the user and C refers to cell type proportion matrix and #T to number of cell types. Notably, Deblender is a complete method, but the partial deconvolution can be done separately and in the context of this study, it is used as expression deconvolution method.

Table 1.

Summary of the tested deconvolution methods

MethodInputTypeAvailability
RodeoCexpressionR/Rodeo
cs-lsfitCexpressionR/CellMix
cs-qprogCexpressionR/CellMix
LRCDECexpressionR/LRCDE
csSAMCexpressionR/csSAM
DeblenderCcompleteMatlab
CDSeq#TcompleteMatlab, Octave, R
LinSeed#TcompleteR/linseed
Deconf#TcompleteR/CellMix
MethodInputTypeAvailability
RodeoCexpressionR/Rodeo
cs-lsfitCexpressionR/CellMix
cs-qprogCexpressionR/CellMix
LRCDECexpressionR/LRCDE
csSAMCexpressionR/csSAM
DeblenderCcompleteMatlab
CDSeq#TcompleteMatlab, Octave, R
LinSeed#TcompleteR/linseed
Deconf#TcompleteR/CellMix

Column ’Input’ describes required input data from the user and C refers to cell type proportion matrix and #T to number of cell types. Notably, Deblender is a complete method, but the partial deconvolution can be done separately and in the context of this study, it is used as expression deconvolution method.

Close
This Feature Is Available To Subscribers Only

Sign In or Create an Account

Close

This PDF is available to Subscribers Only

View Article Abstract & Purchase Options

For full access to this pdf, sign in to an existing account, or purchase an annual subscription.

Close