sRNAtoolBox

sRNAtoolbox is a collection of several tools for RNA analysis. It is implemented into a webserver, a virtual machine, and some of the programs can be furthermore downloaded as standalone versions. Briefly, sRNAtoolbox contains the following tools:

  1. sRNAbench: expression profiling of small RNAs, prediction of novel microRNAs, analysis of isomiRs, genome mapping and read length statistics. The samples are analyzed individually. Note that sRNAbench was published before as the replacement for miRanalyzer (sRNAbench), but later it was incorporated into the sRNAtoolbox collection of sRNA tools.
  2. sRNAde: detection of differentially expressed small RNAs based on three commonly used programs:DESeqedgeR, and NOISeq. To our knowledge it is the first tool that determines a consensus of differentially expressed sRNA.
  3. miRNAgFree: prediction of novel microRNAs without a genome assembly, being designed therefore for the usage in non-model species.
  4. sRNAblast: aimed to determine the origin of unmapped or unassigned reads by means of a blast search against a local nr/nt database. The results can either point towards contamination sources or biological meaningful information like the presence of unexpected viral or bacterial RNA molecules.
  5. miRNAconsTarget: consensus target prediction on user provided input data based on Miranda , PITA and TargetSpy for animal microRNAs.
  6. sRNAjBrowser: visualization of sRNA expression data in a genome context using jBrowse.
  7. sRNAjBrowserDE: visualization of differential expression as a function of read length in a genome context using jBrowse.
  8. sRNAfuncTerms: enrichment of functional annotations in target genes not only for a set of microRNAs, but also for all its combinations (microRNA modules)
  9. sRNAhelper: several tools that can help the user to populate the local database and to obtain the format required by some programs.
  10. sRNAfuncTargets (workflow): cross-species microRNA target prediction and enrichment analysis of functional annotations.