RSeqFlow
A comprehensive R pipeline for processing RNA-Seq datasets from count files (or tables) in non-model organisms comprising:
- Read/construct a count table from RNA-seq mappings
- Quality control and gene filtering
- Normalisation and biologically relevant differential expression
- Correlation analyses for clustering
- Co-expression networks, including hubs and subgraphs
- Profiling outstanding genes.
Basic Information
| Repository | https://github.com/mgclaros/RSeqFlow |
| Documentation | https://github.com/mgclaros/RSeqFlow/blob/main/README.md |
| Seminar | Gonzalo Claros presents the tool RSeqFlow |
| Main publication (DOI) | 10.3390/plants12162894 view |
| Contact email | claros@uma.es |
| Authors/Maintainers | M. Gonzalo Claros Díaz |
| Type of application | R/python package |
| Programming languages | RBASH / Shell |
| Keywords | Omics, Computational Methods, Resources, Transcriptomics, RNA Sequencing (RNA-seq), Data Analysis, Bioinformatics Software and Tools, Analysis packages (R, Python, etc.), Applications of Computational Biology, Expression Profiling, Plant genomics |
Technical details
| Input file formats | csv, tsv |
| Output file formats | tsv, html |
| Software compatibility | Linux, Mac, Windows |
| Hardware requirements | Nothing special |
| Type of containerization | None |
| Wrapper type | None |
| Compatible tools | |
| Funding resource | National competitive funding, Regional/local competitive funding |
| Funding support |
Statistics
| Unique users (last 12 months) | |
| Unique users (since first release) | |
| Software downloads (last 12 months) | |
| Software downloads (since first release) | |
| Jobs submitted (last 12 months) | |
| Jobs submitted (since first release) | |
| Repository clones (last 12 months) | |
| Repository clones (since first release) | |
| Citations (last 12 months) | <100 (~1 as of 15/10/2026) |
| Citations (since first release) | <100 (5 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) |