regsplice: Lasso-Based Methods for Detection of Differential Exon Usage

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Statistical methods for detection of differential exon usage in RNA-seq and exon microarray data sets, using L1 regularization (lasso) to improve power.

Author
Lukas M. Weber [aut, cre]
Date of publication
None
Maintainer
Lukas M. Weber <lukmweber@gmail.com>
License
MIT + file LICENSE
Version
1.0.0
URLs

View on Bioconductor

Man pages

createDesignMatrix
Create design matrix.
filterLowCounts
Filter low-count exons.
filterZeros
Filter zero-count exons.
fitRegMultiple
Fit models.
initializeResults
Initialize RegspliceResults object.
LRTests
Calculate likelihood ratio tests.
regsplice
Wrapper function to run regsplice.
RegspliceData
RegspliceData objects.
RegspliceResults
RegspliceResults objects.
runNormalization
Calculate normalization factors.
runVoom
Calculate 'voom' transformation and weights.
summaryTable
Summary table.

Files in this package

regsplice/DESCRIPTION
regsplice/LICENSE
regsplice/NAMESPACE
regsplice/NEWS
regsplice/R
regsplice/R/LRTests.R
regsplice/R/class_RegspliceData.R
regsplice/R/class_RegspliceResults.R
regsplice/R/createDesignMatrix.R
regsplice/R/filterLowCounts.R
regsplice/R/filterZeros.R
regsplice/R/fitting_functions_multiple_genes.R
regsplice/R/fitting_functions_single_gene.R
regsplice/R/helper_functions.R
regsplice/R/initializeResults.R
regsplice/R/regsplice_wrapper.R
regsplice/R/runNormalization.R
regsplice/R/runVoom.R
regsplice/R/summaryTable.R
regsplice/build
regsplice/build/vignette.rds
regsplice/inst
regsplice/inst/doc
regsplice/inst/doc/regsplice-workflow.R
regsplice/inst/doc/regsplice-workflow.Rmd
regsplice/inst/doc/regsplice-workflow.pdf
regsplice/inst/extdata
regsplice/inst/extdata/data_glmnet_error_example.txt
regsplice/inst/extdata/design_matrix_example.txt
regsplice/inst/extdata/vignette_counts.txt
regsplice/inst/extdata/vignette_truth.txt
regsplice/man
regsplice/man/LRTests.Rd
regsplice/man/RegspliceData.Rd
regsplice/man/RegspliceResults.Rd
regsplice/man/createDesignMatrix.Rd
regsplice/man/filterLowCounts.Rd
regsplice/man/filterZeros.Rd
regsplice/man/fitRegMultiple.Rd
regsplice/man/initializeResults.Rd
regsplice/man/regsplice.Rd
regsplice/man/runNormalization.Rd
regsplice/man/runVoom.Rd
regsplice/man/summaryTable.Rd
regsplice/tests
regsplice/tests/testthat
regsplice/tests/testthat.R
regsplice/tests/testthat/test_design_matrices.R
regsplice/tests/testthat/test_filtering.R
regsplice/tests/testthat/test_glmnet_error_example.R
regsplice/tests/testthat/test_input_data_formats.R
regsplice/tests/testthat/test_input_data_preparation.R
regsplice/tests/testthat/test_normalization.R
regsplice/tests/testthat/test_summary_table.R
regsplice/tests/testthat/test_vignette_example.R
regsplice/tests/testthat/test_voom.R
regsplice/tests/testthat/test_when_null_selected_options.R
regsplice/tests/testthat/test_wrapper_function.R
regsplice/vignettes
regsplice/vignettes/regsplice-workflow.Rmd