Package: SplicingFactory 1.15.0
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_1.15.0.tar.gz
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SplicingFactory.pdf |SplicingFactory.html✨
SplicingFactory/json (API)
NEWS
| # 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
- tcga_brca_luma_dataset - TCGA Luminal A breast cancer dataset
On BioConductor:SplicingFactory-1.15.0(bioc 3.21)SplicingFactory-1.14.0(bioc 3.20)
transcriptomicsrnaseqdifferentialsplicingalternativesplicingtranscriptomevariantgini-indexrna-seqshannon-entropysimpson-indexsplicing
Last updated 5 months agofrom:ac49427bf6. Checks:8 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 25 2025 |
| R-4.5-win | OK | Feb 25 2025 |
| R-4.5-mac | OK | Feb 25 2025 |
| R-4.5-linux | OK | Feb 25 2025 |
| R-4.4-win | OK | Feb 25 2025 |
| R-4.4-mac | OK | Feb 25 2025 |
| R-4.3-win | OK | Feb 25 2025 |
| R-4.3-mac | OK | Feb 25 2025 |
Exports:calculate_differencecalculate_diversitycalculate_entropycalculate_ginicalculate_inverse_simpsoncalculate_simpson
Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVector
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 |
