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1. plasslab/SCALPEL plasslab/SCALPEL Public

   Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline.

   R 31 3

2. rajewsky-lab/SPACEGERM rajewsky-lab/SPACEGERM Public archive

   SPACEGERM shiny app (archived, see GitLab for active fork)

   R

3. rajewsky-lab/mirdeep2 rajewsky-lab/mirdeep2 Public

   Discovering known and novel miRNAs from small RNA sequencing data

   Perl 159 54

4. rajewsky-lab/find_circ2 rajewsky-lab/find_circ2 Public

   Find circRNAs in RNA-seq data.

   Python 15 7

5. BIMSBbioinfo/ciRcus BIMSBbioinfo/ciRcus Public

   An R package for annotation of circular RNAs

   R 11 5

6. microSNPscore microSNPscore Public archive

   mirSVR-based tool to predict the effects of SNPs on miRNA:target interactions [migrated to gitlab]

   C++