regsplice: L1-regularization based methods for detection of differential splicing
Version 1.2.0

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

AuthorLukas M. Weber [aut, cre]
Bioconductor views AlternativeSplicing DifferentialExpression DifferentialSplicing ExonArray ExperimentalDesign Microarray RNASeq Sequencing Software
Date of publicationNone
MaintainerLukas M. Weber <lukmweber@gmail.com>
LicenseMIT + file LICENSE
Version1.2.0
URL https://github.com/lmweber/regsplice
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("regsplice")

Getting started

Example workflow for regsplice package

Popular man pages

createDesignMatrix: Create design matrix.
filterLowCounts: Filter low-count exons.
filterZeros: Filter zero-count exons.
RegspliceResults: RegspliceResults objects.
runNormalization: Calculate normalization factors.
runVoom: Calculate 'voom' transformation and weights.
summaryTable: Summary table.
See all...

All man pages Function index File listing

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.

Functions

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

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/LRTests.R
R/class_RegspliceData.R
R/class_RegspliceResults.R
R/createDesignMatrix.R
R/filterLowCounts.R
R/filterZeros.R
R/fitting_functions_multiple_genes.R
R/fitting_functions_single_gene.R
R/helper_functions.R
R/initializeResults.R
R/regsplice_wrapper.R
R/runNormalization.R
R/runVoom.R
R/summaryTable.R
build
build/vignette.rds
inst
inst/doc
inst/doc/regsplice-workflow.R
inst/doc/regsplice-workflow.Rmd
inst/doc/regsplice-workflow.pdf
inst/extdata
inst/extdata/data_glmnet_error_example.txt
inst/extdata/design_matrix_example.txt
inst/extdata/vignette_counts.txt
inst/extdata/vignette_truth.txt
man
man/LRTests.Rd
man/RegspliceData.Rd
man/RegspliceResults.Rd
man/createDesignMatrix.Rd
man/filterLowCounts.Rd
man/filterZeros.Rd
man/fitRegMultiple.Rd
man/initializeResults.Rd
man/regsplice.Rd
man/runNormalization.Rd
man/runVoom.Rd
man/summaryTable.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_design_matrices.R
tests/testthat/test_filtering.R
tests/testthat/test_glmnet_error_example.R
tests/testthat/test_input_data_formats.R
tests/testthat/test_input_data_preparation.R
tests/testthat/test_normalization.R
tests/testthat/test_subsetting.R
tests/testthat/test_summary_table.R
tests/testthat/test_vignette_example.R
tests/testthat/test_voom.R
tests/testthat/test_when_null_selected_options.R
tests/testthat/test_wrapper_function.R
vignettes
vignettes/regsplice-workflow.Rmd
regsplice documentation built on May 20, 2017, 10:22 p.m.

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