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Tools

List of Tools and Software Packages developed in the Kreutz-Lab

Tool zur Qualitätskontrolle von Omics-Daten:

omicscharacterization.imbi.uni-freiburg.de

 

Preprint: Characterizing the omics landscape based on 10,000+ datasets

www.researchsquare.com/article/rs-3978776/v1

 

R-package for RTF Modelling:

github.com/kreutz-lab/rtf

 

R-Package "Loci of Enhanced Significance" (Bioconductor)

bioconductor.jp/packages/release/bioc/manuals/les/man/les.pdf

 

Package for using R in Matlab:

github.com/kreutz-lab/Rcall

 

R-Package for identification of the optimal imputation method:

github.com/kreutz-lab/DIMAR

 

R-Package for statistical analyses of zero-inflated data:

github.com/kreutz-lab/zitools

 

R-Package for simulating benchmark data:

github.com/kreutz-lab/simFrB

 

R-Package for the analysis of hierarchical count data:

github.com/kreutz-lab/CountSpores

 

Agent-based model for finding an optiomal COVID-19 surveillance strategie:

github.com/kreutz-lab/COVID19Surveillance

Bioconductor R-package for Data Normalization

This package provides a normalization method for omics data where a few features are highly expressed. Then the traditional quantile normalization that is based on ranking proteins is not applicable any more. We developed a mean balanced quantile normalization that is also applicable in such settings.

Installation: https://www.bioconductor.org/packages/release/bioc/html/MBQN.html

Publication: Brombacher, E., Schad, A., & Kreutz, C. (2020). Tail‐Robust Quantile Normalization. Proteomics, 20(24), 2000068.

Data2Dynamics

In this project, we develop and extend the Data2Dynamics modelling environment which is a high-performance expert implementation for mathematical modelling.

Link: D2D repository at github

Responsible: Lukas Refisch, Janine Egert, Clemens Kreutz

Our collaborators: Jens Timmer, Andreas Raue


Benchmarking Wiki

In this project, we started to develop a wiki as a repository for published benchmark studies. We intend to collect insights from literature obtained by comparing the performance of computational approaches.

The benchmarking wiki also offers the opportunity to publish (possibly small or unpublished) own results.

Everybody is welcome to contribute!

Link: Benchmark Wiki

Responsible: Clemens Kreutz


Anfahrt/Location (klick on the image):

Address

Institut of Medical Biometry and Statistics
- Methods of Systems Biomedicine / Kreutz-Lab -

Stefan-Meier Str. 26

79104 Freiburg