R-universe search: topic:splicing

Showing 3 of total 3 results (show query)

bioc

FRASER:Find RAre Splicing Events in RNA-Seq Data

Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.

Maintained by Christian Mertes. Last updated 5 months ago.

rnaseq alternativesplicing sequencing software genetics coverage aberrant-splicing diagnostics outlier-detection rare-disease rna-seq splicing openblas cpp

41 stars 8.50 score 155 scripts

bioc

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.

Maintained by Endre Sebestyen. Last updated 5 months ago.

transcriptomics rnaseq differentialsplicing alternativesplicing transcriptomevariant gini-index rna-seq shannon-entropy simpson-index splicing

4 stars 5.20 score 1 scripts

bioc

VaSP:Quantification and Visualization of Variations of Splicing in Population

Discovery of genome-wide variable alternative splicing events from short-read RNA-seq data and visualizations of gene splicing information for publication-quality multi-panel figures in a population. (Warning: The visualizing function is removed due to the dependent package Sushi deprecated. If you want to use it, please change back to an older version.)

Maintained by Huihui Yu. Last updated 5 months ago.

rnaseq alternativesplicing differentialsplicing statisticalmethod visualization preprocessing clustering differentialexpression kegg immunooncology 3s-scores alternative-splicing ballgown rna-seq splicing sqtl statistics

3 stars 4.78 score 3 scripts