tappAS
tappAS is a free Java GUI application designed for the functional analysis of RNA-Seq data at the isoform level, focusing on alternative splicing and UTR processing. It supports project-based workflows, requiring an experimental design file, a transcript-level expression matrix, and an annotation file. The application offers extensive data analysis tools and provides comprehensive interactive data visualization options. tappAS is compatible with most modern computers and includes customizable data tables, export features, and user-friendly GUI elements.
Basic Information
| Repository | https://github.com/ConesaLab/tappAS |
| Documentation | https://app.tappas.org/overview/ |
| Main publication (DOI) | 10.1186/s13059-020-02028-w view |
| Contact email | conesalab@gmail.com |
| Authors/Maintainers | Ana Conesa |
| Type of application | Desktop application |
| Programming languages | RJavaHTMLMySQL |
| Keywords | Omics, Computational Methods, Resources, Transcriptomics, RNA Sequencing (RNA-seq), Data Analysis, Bioinformatics Software and Tools, Annotation tools, Data Visualization, Genomics, Functional genomics, Functional annotation, Bioinformatics Infrastructure, Expression Profiling, Computational models and simulations, Gene regulatory networks, Desktop application, Genomic Annotation, Statistical Methods for Biology, Frequentist analysis, Experimental design, Pathway analysis, Biological Ontologies, Multivariate statistics, Long-read sequencing |
Technical details
| Input file formats | csv, gff, gtf |
| Output file formats | |
| Software compatibility | Linux, Mac, Windows |
| Hardware requirements | Minimum of 8 GBs of memory, Minimum of 4 cores (multi-core CPU or single core CPUs), Minimum of 20 GBs of available unused disk space |
| Type of containerization | None |
| Wrapper type | None |
| Compatible tools | SQANTI3, IsoAnnot (IsoAnnotLite) |
| Funding resource | National competitive funding, EU funding |
| Funding support |
Statistics
| Unique users (last 12 months) | |
| Unique users (since first release) | 100-1000 |
| Software downloads (last 12 months) | |
| Software downloads (since first release) | 100-1000 |
| Jobs submitted (last 12 months) | |
| Jobs submitted (since first release) | |
| Repository clones (last 12 months) | <100 |
| Repository clones (since first release) | <100 |
| Citations (last 12 months) | <100 (~10 as of 15/10/2026) |
| Citations (since first release) | <100 (70 as of 15/10/2026) |
| Early-stage researcher effort (development) | |
| Early-stage researcher effort (maintenance) | |
| Technician-supported effort (development) | |
| Technician-supported effort (maintenance) | |
| Other effort (development) | |
| Other effort (maintenance) | |
| Total effort (development) | |
| Total effort (maintenance) |