Package: SplicingFactory 1.13.0

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:Peter A. Szikora [aut], Tamas Por [aut], Endre Sebestyen [aut, cre]

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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

Datasets:

tcga_brca_luma_dataset - TCGA Luminal A breast cancer dataset

On BioConductor:SplicingFactory-1.13.0(bioc 3.20)SplicingFactory-1.12.0(bioc 3.19)

bioconductor-package

6 exports 0.82 score 28 dependencies

Last updated 2 months agofrom:cb30fa4b70

Exports:calculate_difference calculate_diversity calculate_entropy calculate_gini calculate_inverse_simpson calculate_simpson

Dependencies:abind askpass Biobase BiocGenerics crayon curl DelayedArray GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite lattice Matrix MatrixGenerics matrixStats mime openssl R6 S4Arrays S4Vectors SparseArray SummarizedExperiment sys UCSC.utils XVector zlibbioc

SplicingFactory

Péter Szikora, Tamás Pór, Endre Sebestyén

Rendered fromSplicingFactory.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2021-07-17
Started: 2020-06-13

Citation

Development and contributors

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