hibeRNAte: a framework for small RNA analysis
- Web-based interface
- NGS read library pre-processing and data format conversion
- Small RNA knowledge base search
- Short-read mapping to genomic reference
- De novo sRNA categorization
- Argonaute-sRNA affinity inference
- Transcriptional and post-transcriptional target prediction
- Differential expression analysis
- Gene ontology analysis
- Network analysis
- In silico simulation of sRNA networks
SAILS: a tool for AGO-sRNA affinity inference
- Web-based interface
- Machine learning models to predict kinship between small RNA and argonaute proteins from sequence alone
- Inference system for small RNA mode of action from sequence alone
MethBrowser: a genome browser for epigenetics
- Web-based interface
- Visualization of methylomes in populations
- Visualization of small RNA abundance
- Visualization of genome annotations
- Genome-wide querying by genomic coordinates or gene ID
- Functionalities to download data in tabular format
XpressR: A tool for gene expression exploration and visualization
- Web-based interface
- Querying by model metadata and genes of interest
- Output metadata for models retrieved
- Interactive boxplots with RPKM values per model, coloured by group
- Barplots with RPKM values per gene or per model
- Correlation analysis for expression among selected models
AbPTM: a tool to predict antibody residues prone to post-translational modifications
- Web-based interface
- Numbering and antigen receptor classification
- Canonical loop structure annotation (including the detection of the heavy chain, light chain and CDRs)
- Detection of PTM prone residues via an embedded motif search
- Indication of residue physicochemical properties using multiple popular schemes
