Introduction | Example workflow | Data set | Exon microarray data | Workflow | Load data and create condition vector | Run workflow with wrapper function | Summary table of results | Run workflow using functions for individual steps | Create RegspliceData object | Filter zero-count exon bins | Filter low-count exons | Calculate normalization factors | 'voom' transformation and weights | Initialize RegspliceResults object | Fit models | Calculate likelihood ratio tests | Analyze results | Summary of all significant genes | Contingency table | Additional information | Additional user options | Design matrices
Package: regsplice 1.38.1
Lukas M. Weber
regsplice: L1-regularization based methods for detection of differential splicing
Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.
Authors:
regsplice_1.38.1.tar.gz
regsplice_1.38.1.zip(r-4.7-any)regsplice_1.38.1.zip(r-4.6-any)regsplice_1.38.1.zip(r-4.5-any)
regsplice_1.38.1.tgz(r-4.6-any)regsplice_1.38.1.tgz(r-4.5-any)
regsplice_1.38.1.tar.gz(r-4.7-any)regsplice_1.38.1.tar.gz(r-4.6-any)
regsplice_1.38.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
regsplice/json (API)
| # Install 'regsplice' in R: |
| install.packages('regsplice', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lmweber/regsplice/issues
On BioConductor:regsplice-1.39.1(bioc 3.24)regsplice-1.38.1(bioc 3.23)
immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicingsequencingrnaseqmicroarrayexonarrayexperimentaldesignsoftware
Last updated from:abdeda7733 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 153 | ||
| linux-devel | NOTE | 294 | ||
| source / vignettes | OK | 221 | ||
| linux-release | NOTE | 277 | ||
| macos-release | NOTE | 234 | ||
| macos-oldrel | NOTE | 266 | ||
| windows-devel | NOTE | 208 | ||
| windows-release | NOTE | 225 | ||
| windows-oldrel | NOTE | 273 | ||
| wasm-release | OK | 101 |
Exports:assayscolDatacountsDatacreateDesignMatrixdf_testsfilterLowCountsfilterZerosfitFullMultiplefitNullMultiplefitRegMultiplegene_IDsinitializeResultsLR_statsLRTestsp_adjp_valsregspliceRegspliceDataRegspliceResultsrowDatarunNormalizationrunVoomsummaryTableweightsData
Dependencies:abindBiobaseBiocGenericscodetoolsDelayedArrayedgeRforeachgenericsGenomicRangesglmnetIRangesiteratorslatticelimmalocfitMatrixMatrixGenericsmatrixStatspbapplyRcppRcppEigenS4ArraysS4VectorsSeqinfoshapeSparseArraystatmodSummarizedExperimentsurvivalXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create design matrix. | createDesignMatrix |
| Filter low-count exons. | filterLowCounts |
| Filter zero-count exons. | filterZeros |
| Fit models. | fitFullMultiple fitNullMultiple fitRegMultiple |
| Initialize RegspliceResults object. | initializeResults |
| Calculate likelihood ratio tests. | LRTests |
| Wrapper function to run regsplice. | regsplice |
| RegspliceData objects. | assays,RegspliceData-method colData,RegspliceData-method countsData countsData,RegspliceData-method RegspliceData RegspliceData-class rowData,RegspliceData-method weightsData weightsData,RegspliceData-method [,RegspliceData,ANY,ANY,ANY-method |
| RegspliceResults objects. | df_tests df_tests,RegspliceResults-method gene_IDs gene_IDs,RegspliceResults-method LR_stats LR_stats,RegspliceResults-method p_adj p_adj,RegspliceResults-method p_vals p_vals,RegspliceResults-method RegspliceResults RegspliceResults-class |
| Calculate normalization factors. | runNormalization |
| Calculate 'voom' transformation and weights. | runVoom |
| Summary table. | summaryTable |
