A list of alternative splicing analysis resources
Review 1 Review 2 Review 3 Review 4 Review 5 Review 6
- URL
- PubMed
- GitHub
- [Pubmed HISAT-3N] (https://pubmed.ncbi.nlm.nih.gov/34103331/)
featureCounts is a part of Subread to count features expression
The R code is in the supplementary materials
Based on not supporting tool MISO
IRFinder is not maintained
Not maintained.
Jutils/MntJULiP: A visualization toolkit for differential alternative splicing events/Now with covariates
KISSDE for differential splicing analysis
Part of TAP pipeline
spliceR: a tool for alternative splicing events, differential splicing detection, and isoform switching
Not maintained.
- Cufflinks assembles transcriptomes from RNA-Seq data and quantifies their expression.
- Cuffcompare compares the assembled transcriptomes
- Cuffmerge merges the tranacriptomes from multiple RNA-Seq libraries
- Cuffquant computes the gene and transcript expression profiles
- Cuffdiff compares expression levels of genes and transcripts in RNA-Seq
- Cuffnorm normalizes the expression levels
- URL
- PubMed
- GitHub
SEVA is implemented in the R package GSReg
The list of R scripts
The list of Python scripts
sleuth is a differential isoform expression tool after kallisto analysis
Not maintained
The variant of the tools is pRSEM: an isoform quantification with a complementary data
No documentation
Archived
The list of Perl scripts
Part of the sysSeq package. No easily accessible documentation
The tool can quantify exon expression
An R script
A list of scripts
The code is upon request
The tool also detects differentially regulated exons. MISO also presents sashimi plots for exon expression visualisation. No longer maintained.
Redirects to ESEfinder
- BioRxiv The code will be after publication
No easily accessible documentation
The code for the model
The model
The model
The code
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Limited access
RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer
rPGA: a hidden splicing variations
No code provided
No documentation
- Pubmed
- [URL Not available]http://bioserv.mps.ohio-state.edu/dsRBPBind
The code is upon request
The Python script with no documentation
Last release: 2019, February, 20th
No code
Last release: 2021, February
SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors
Last release: 2016
No documentation
jcast: takes in alternative splicing events and returns custom protein sequence databases for isoform analysis
QUILTS: the identification of novel proteins, resulting from single nucleotide variants, splice variants, and fusion genes
- URL Not available
- PubMed
- GitHub - on a very early stage
TopPG: a proteogenomic tool for generating proteoform sequence databases with genetic alterations and alternative splicing events
EXPANSION: a webserver to explore the functional consequences of protein-coding alternative splice variants in cancer genomics
Single-cell data (much much more here https://www.scrna-tools.org/)
Long reads (much much more here https://long-read-tools.org/)
ASAPA: a pipeline that identifies the links among alternative splicing, alternative transcription initiation and alternative polyadenylation
A code is not found
FLAME: a bioinformatics pipeline for alternative splicing analysis of gene-specific or transcriptome-wide long-read sequencing data
Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing
- PubMed
- [URL Not available](http://mlda.swu.edu.cn/codes.php? name=IsoFun)
SpliceTools: a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing
No code available
The code is not available
circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging
FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing
Kallisto-Splice is part of a tool for a splice-aware mapping
For RNA-Seq only
ACEScan: the algorithm for prediction of conserved alternatively spliced exons from pairs of conserved mouse/human exons
The code is upon request
ASES: a tool for assessing the impact of alternative splicing, initiation and termination of transcription on protein diversity in evolution
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34563123/)
- [GitHub] (https://github.com/itmat/CAMPAREE)
Last release
eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping
SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data
UNCOVER: the algorithm for predicting conserved alternatively spliced exons (and retained introns) in orthologous intron pairs (Upon request)
- PubMed
- FTP
CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris)
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs
FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels
IDeAS: an interactive database for dysregulated alternative splicing in cancers across Chinese and western patients
oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species
ProSAS: a database of the effects of alternative splicing events on the structure of the resulting protein isoforms.
The code is not found
recount3: an online resource consisting of RNA-seq gene, exon, and exon-exon junction counts as well as coverage
- Pubmed
- [URL] Does not work
SpliceAid: a database of experimentally proven RNA target motifs bound by splicing proteins in human
scTEA-db: a database of novel terminal exon isoforms identified from human single cell transcriptomes
surfaltr: An R/Bioconductor package to benchmark surface protein isoforms by rapid prediction and visualization of transmembrane topologies
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34674629/)
- [URL] (http://bioinfolab.unl.edu/emlab/consemble/ )
- [Pubmed] (https://pubmed.ncbi.nlm.nih.gov/34033544/)
- [GitHub] (https://github.com/jzbio/MultiTrans)
- Comparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders
- Benchmarking deep learning splice prediction tools using functional splice assays
- Performance evaluation of computational methods for splice-disrupting variants and improving the performance using the machine learning-based framework
- Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers
- A comprehensive benchmarking of differential splicing tools for RNA-seq analysis at the event level
- Alternative splicing analysis benchmark with DICAST
- Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads
- Exploring differential exon usage via short- and long-read RNA sequencing strategies
- Enhancing novel isoform discovery: leveraging nanopore long-read sequencing and machine learning approaches
- Comprehensive benchmark of differential transcript usage analysis for static and dynamic conditions