PyHIST is a Histological Image Segmentation Tool: a lightweight semi-automatic pipeline to extract tiles with foreground content from SVS histopathology whole image slides (with experimental support for other formats). It is intended to be an easy-to-use tool to preprocess histological image data for usage in machine learning tasks.

sQTLseekeR is a R package to detect splicing QTLs (sQTLs), which are variants associated with change in the splicing pattern of a gene. Here, splicing patterns are modeled by the relative expression of the transcripts of a gene. For more information about the method and performance see article:

Selenoprofiles is a pipeline for profile-based protein finding in genomes.

compmerge is a program that tries to solve the same problem as cuffmerge. It is not limited to cufflinks models and transcripts, but can work with any .gtf file. It merges the spliced transcripts that have a compatible intron structure and merges the monoexonic transcripts based on simple stranded overlap. The output is a .gtf file of merged transcripts.

SECISaln will predict a SECIS element in the query sequence, split it into its constituent parts and align these against a precompiled database of eukaryotic SECIS elements. The user can choose whether the database sequences are sorted by protein family or by species, thereby offering the possibility of comparing the submitted sequence to other, known SECISes. In addition, SECISaln returns a graphical image of the predicted structure of the user-submitted sequence as well as a multiple…

overlap is a program that computes the overlap between two sets of genomic features. More precisely it takes two gff files of genomic features as input and for each feature of the first set, says whether it is overlapped by a feature of the second set (basic mode, however more and more precise information can be retrieved).