| Tail Tools | PAT-Seq data analysis software. Call polyadenylation sites from PAT-Seq data. Produce gene and site-level read counts. Produce average poly(A) tail length per gene and per site. Detect differential poly(A) tail length and alternative polyadenylation. |
| Varistran | R package providing a variance stabilizing transformation of RNA-seq data, and RNA-seq visualization tools. |
| Topconfects | Bioconductor pacakge for computing confidence bounds on differential gene expression. More advanced applications include detecting shifting in the preferred 3'-ends of transcripts. |
| Weitrix | Bioconductor package for working with a matrix of data with precision weights. This can be used with the output of Tail Tools to detect differential poly(A) tail length and alternative polyadenylation. |
| polyApipe | Python/R software for detecting alternative polyadenylation in 10X single cell data. |