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

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

AuthorLukas M. Weber [aut, cre]
Date of publicationNone
MaintainerLukas M. Weber <lukmweber@gmail.com>
LicenseMIT + file LICENSE
Version1.0.0
https://github.com/lmweber/regsplice

View on Bioconductor

Functions

assays,RegspliceData-method Man page
colData,RegspliceData-method Man page
countsData Man page
countsData,RegspliceData-method Man page
createDesignMatrix Man page
df_tests Man page
df_tests,RegspliceResults-method Man page
filterLowCounts Man page
filterZeros Man page
fitFullMultiple Man page
fitNullMultiple Man page
fitRegMultiple Man page
gene_IDs Man page
gene_IDs,RegspliceResults-method Man page
initializeResults Man page
LR_stats Man page
LR_stats,RegspliceResults-method Man page
LRTests Man page
p_adj Man page
p_adj,RegspliceResults-method Man page
p_vals Man page
p_vals,RegspliceResults-method Man page
regsplice Man page
RegspliceData Man page
[,RegspliceData,ANY,ANY,ANY-method Man page
RegspliceData-class Man page
RegspliceResults Man page
RegspliceResults-class Man page
rowData,RegspliceData-method Man page
runNormalization Man page
runVoom Man page
summaryTable Man page
weightsData Man page
weightsData,RegspliceData-method Man page

Files

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

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