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Software

Tools

PPaxe

Website | Publication | Code

PPaxe is a tool to retrieve protein-protein interactions and calculate protein/gene symbol ocurrence in the scientific literature (PubMed & PubMedCentral). Contains two Python modules, core and report, and a Python script, ppaxe.

PlanNET

Website | Publication | Code

PlanNET is a web application that stores predicted Schmidtea mediterranea protein-protein interactions (PPI) projected over a Human ppi network

RPGeNet

Website | Publication

RPGeNet is a web application to explore the retinitis pigmentosa gene interaction network. Version 1 interactions core skeleton network was built upon 110 RP/LCA driver genes, but the new major upgrade to version 2 engine includes 276 retinal dystrophies driver genes.

SiNoPsis

Website | Publication

This web application is specialized to characterize annotated gene or genomic coordinates (GRCh37/hg19) in terms of Transcription Factor binding sites, histone marks, open-chromatin states, as well as SNPs linkage desequilibrium and eQTL properties.

gff2aplot

Website | Publication

gff2aplot is a program to visualize the alignment of two sequences together with their annotations. Input for the program consists of single or multiple files in GFF-format which specify the alignment coordinates and annotation features of both sequences. Output is in PostScript format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis.

gff2ps

Website | Publication

gff2ps is a program for visualizing annotations of genomic sequences. The program takes as input the annotated features on a genomic sequence in GFF format, and produces a visual output in PostScript. It can be used in a very simple way, because it assumes that the GFF file itself carries enough formatting information, but it also allows through a number of options and/or a configuration file, for a great degree of customization.

CompGen Main Repository

Github

Website

Computational Genomics Lab code repository.


Page last modified on Monday 28 of January, 2019 12:06:11 CET