awesome-alternative-splicing
Alternative Splicing Resource
A resource for software and information about alternative splicing in RNA sequencing data.
Alternative splicing resource
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awesome-alternative-splicing / Software | |||
| 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 | 125 | over 2 years ago | 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 | 65 | over 5 years ago | 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 | ||
| rmats2sashimiplot | 135 | 11 months ago | visualize rMATS output using sashimi plots |
| SAW | identify splicing events from RNA-Seq data | ||
| Scripture | reconstruct transcript isoforms | ||
| SingleSplice | 21 | over 9 years ago | 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 | 264 | over 1 year ago | identify alternative splicing |
| TopHat | map splice junctions for RNA-Seq reads | ||
awesome-alternative-splicing / Databases | |||
| 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 | ||
danielecook/awesome-bioinformatics