To address the pandemic of the Coronavirus Disease-2019 (COVID-19), drug repurposing can be a helpful approach since it offers the possibility to find alternative fields of application for already approved drugs. CoVex is the first network and systems medicine online data analysis platform that integrates virus-human interaction data for SARS-CoV-2 and SARS-CoV. It is available […]
Domain Interaction Graph Guided ExploreR (DIGGER) integrates protein-protein interactions and domain-domain interactions into a joint graph and maps interacting residues to exons. DIGGER allows the users to query exons or isoforms individually or as a set to visually explore their interactions. Further information can be found here.
EpiGEN is a Python pipeline for simulating epistasis data. It supports epistasis models of arbitrary size, which can be specified either extensionally or via parametrized risk models. Moreover, the user can specify the minor allele frequencies (MAFs) of both noise and disease SNPs, and provide a bias target distribution for the generated phenotypes to simulate
NeDRex is an integrative and interactive platform for network-base drug repurposing and disease module identification. More information, tutorials and a download link for the app can be found here.
sPLINK (safe PLINK) allows the federated, privacy-preserving analysis of GWAS data. It works on distributed datasets without exchanging raw data and is robust against imbalanced phenotype distributions across cohorts. Federated and user-friendly analysis with sPLINK, thus, has the potential to replace meta-analysis as the gold standard for collaborative GWAS. The tool is available online here.
DICAST comprises several alternative splicing event detection tools for analyzing RNA-Seq data. It can be used as a benchmark to compare the results of the different tools. More information and instructions can be found here.
ASimulatoR is an R package for the simulation of RNA-seq reads with alternative splicing events. It is freely available on GitHub.
Fastlogranktest is a software package providing wicked-fast implementations of the logrank test in C++, R, and Python. The Python package and R package provide wrappers around the C++ implementation. Both offer a fast alternative to the standard logrank-test implementations in the liflines.statistics and survival packages, respectively. All you have to do is install the package
NEASE (Network-based Enrichment method for Alternative Splicing Events) is a Python package for the functional enrichment of alternative splicing events. The tool is available on GitHub.
Spycone is a python package for a splicing-aware analysis of time course data. It is available on Github.
