Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
awesome-alternative-splicing
Alternative splicing resource
https://github.com/HussainAther/awesome-alternative-splicing
- Contributions welcome
- ALEXA-Seq - alternative expression analysis by massively parallel sequencing.
- AltAnalyze - analyze alternative splicing from single-cell and RNA-Seq data.
- Cufflinks - assemble and quantify transcripts.
- DEXSeq - identify differential exon usage.
- flotilla - reproduce machine learning analysis of gene expression and alternative splicing data.
- GMAP and GSNAP - detect complex variants and splicing in short reads, SNP-tolerant.
- G-Mo.R-Se - maps splice junctions to genome.
- HMMSplicer - discovery canonical and non-canonical splice junctions in short read datasets.
- JunctionSeq - identify differential splice junctions.
- MapSplice - map RNA-seq data to reference genome for splice junction discovery.
- MISO - determine alternative splicing expression.
- MMES - statistically determine alternative splicing.
- outrigger - calculate alternative splicing scores of RNA-Seq data based on junction reads and a de novo, custom annotation created with a graph database, especially made for single-cell analyses.
- rMATS - RNA-Seq Multavariate Analysis of Transcript Splicing. [Reading rMATS output](https://www.biostars.org/p/256949/)
- rmats2sashimiplot - visualize rMATS output using sashimi plots.
- SAW - identify splicing events from RNA-Seq data.
- Scripture - reconstruct transcript isoforms.
- SingleSplice - detect biological variation in alternative splicing within a population of single cells.
- SpliceMap - discover and align splice junctions for RNA-Seq reads.
- SpliceR - detect alternative splicing and predict coding potential.
- SplicingCompass - detect differential splicing using RNA-Seq data.
- SplitSeek - predict splice events from RNA-Seq data.
- STAR - identify alternative splicing.
- SUPPA - identify alternative splicing.
- TopHat - map splice junctions for RNA-Seq reads.
- ASIP - Alternative Splicing in Plants.
- ASG - Alternative Splicing Gallery for human genes.
- ASPicDB - Alternative Splicing PredICtion DataBase.
- ENSEMBL - Human and mouse genome annotations.
- FAST DB/Easana - Friendly Alternative Splicing and Transcripts Database.
- Hollywood exon annotation database - A website for querying a relational database of constitutive and alternative human exons, by using biological and descriptive features.
- HS3D - Data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank Rel.123.
- H-DBAS - Human-transcriptome DataBase for Alternative Splicing.
- MAASE - Convenient access, identification, and annotation of alternative splicing events (ASEs), designed specifically with experimentalists in mind.
- Pro-Splicer - Alternative splicing database based on protein, mRNA, and EST Sequences.
- SpliceNest - Visualizing splicing of genes from EST Data for human, mouse, Drodophila and Arabidopsis.