Standard workflow | Input data structure | Data arrangement | Example dataset | Splicing diversity analysis | Importing example data | Data filtering and preprocessing | Transcript diversity calculation | Differential analysis | Session info
Package: SplicingFactory 1.21.0
Endre Sebestyen
SplicingFactory: Splicing Diversity Analysis for Transcriptome Data
The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions.
Authors:
SplicingFactory_1.21.0.tar.gz
SplicingFactory_1.21.0.zip(r-4.7)SplicingFactory_1.21.0.zip(r-4.6)SplicingFactory_1.21.0.zip(r-4.5)
SplicingFactory_1.21.0.tgz(r-4.6-any)SplicingFactory_1.21.0.tgz(r-4.5-any)
SplicingFactory_1.21.0.tar.gz(r-4.7-any)SplicingFactory_1.21.0.tar.gz(r-4.6-any)
SplicingFactory_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SplicingFactory/json (API)
| # Install 'SplicingFactory' in R: |
| install.packages('SplicingFactory', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/esebesty/splicingfactory/issues
Datasets:
- tcga_brca_luma_dataset - TCGA Luminal A breast cancer dataset
On BioConductor:SplicingFactory-1.21.0(bioc 3.24)SplicingFactory-1.20.0(bioc 3.23)
transcriptomicsrnaseqdifferentialsplicingalternativesplicingtranscriptomevariantgini-indexrna-seqshannon-entropysimpson-indexsplicing
Last updated from:bbd6d243e8. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 169 | ||
| linux-devel-x86_64 | OK | 292 | ||
| source / vignettes | OK | 227 | ||
| linux-release-x86_64 | OK | 314 | ||
| macos-release-arm64 | OK | 129 | ||
| macos-oldrel-arm64 | OK | 141 | ||
| windows-devel | OK | 163 | ||
| windows-release | OK | 161 | ||
| windows-oldrel | OK | 168 | ||
| wasm-release | OK | 119 |
Exports:calculate_differencecalculate_diversitycalculate_entropycalculate_ginicalculate_inverse_simpsoncalculate_simpson
Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate splicing diversity changes between two conditions. | calculate_difference |
| Main function for calculating splicing diversity | calculate_diversity |
| Calculate entropy for a vector of transcript-level expression values of one gene. | calculate_entropy |
| Calculate splicing diversity changes between two conditions. | calculate_fc |
| Calculate Gini coefficient for a vector of transcript-level expression values of one gene. | calculate_gini |
| #' Calculate inverse Simpson index for a vector of transcript-level expression values of one gene. | calculate_inverse_simpson |
| Calculate diversity values for a matrix of transcripts. | calculate_method |
| #' Calculate Simpson index for a vector of transcript-level expression values of one gene. | calculate_simpson |
| Calculate p-values using label shuffling. | label_shuffling |
| TCGA Luminal A breast cancer dataset | tcga_brca_luma_dataset |
| Calculate p-values using Wilcoxon rank sum test. | wilcoxon |
