Software & Resources | Scibiome

Spycone

Wed, 14 Sep 2022 00:00:00 +0000

Spycone is a python package for a splicing-aware analysis of time course data. It is available on Github.

DICAST

Tue, 13 Sep 2022 00:00:00 +0000

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.

NeDRex

Tue, 13 Sep 2022 00:00:00 +0000

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.

ASimulatoR

Thu, 25 Aug 2022 00:00:00 +0000

ASimulatoR is an R package for the simulation of RNA-seq reads with alternative splicing events. It is freely available on GitHub.

NEASE

Thu, 25 Aug 2022 00:00:00 +0000

NEASE (Network-based Enrichment method for Alternative Splicing Events) is a Python package for the functional enrichment of alternative splicing events. The package is available on GitHub.

DIGGER

Sat, 01 Aug 2020 00:00:00 +0000

sPLINK

Mon, 08 Jun 2020 00:00:00 +0000

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.

CoVex

Sat, 11 Apr 2020 00:00:00 +0000

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 as interactive webtool. More information and current updates can be found at the CoVex blog at the Chair of Experimental Bioinformatics website.

Scellnetor

Fri, 03 Apr 2020 00:00:00 +0000

Scellnetor is a novel scRNA-seq clustering tool. It allows the analysis of pseudo time-courses in single-cell sequencing data via a network-constrained clustering algorithm. Scellnetor is available as interactive online application at the Scellnetor website.

EpiGEN

Wed, 05 Feb 2020 00:00:00 +0000

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 observation bias. EpiGEN is freely available as python 3 package on GitHub.

Fastlogranktest

Thu, 30 Jan 2020 00:00:00 +0000

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 fastlogranktest and use the method of the same name with exactly the same usage. Furthermore, the Python package and R package provide threading to parallelize the logrank-tests and calculate them even faster with the multi_logrank_test()-method.

The C++ programm itself allows to specify arbitrary group classifications and survival data in a simple tab-separated text-file to run many tests with a single command. The result is provided as another text file with the p-values corresponding to the specified classifications.

BiCoN

Tue, 07 Jan 2020 00:00:00 +0000

BiCoN is a powerful new systems medicine tool to stratify patients while elucidating the responsible disease mechanisms. BiCoN is a network-constrained biclustering approach which restricts biclusters to functionally related genes connected in molecular interaction networks and maximizes the expression difference between two subgroups of patients. A package for network-constrained biclustering of patients and multi-omics data can also be used. Download and installation instructions can be found here.