Tools
List of Tools and Software Packages developed in the Kreutz-Lab
Tool zur Qualitätskontrolle von Omics-Daten: |
Preprint: Characterizing the omics landscape based on 10,000+ datasets |
R-package for RTF Modelling: |
R-Package "Loci of Enhanced Significance" (Bioconductor) |
bioconductor.jp/packages/release/bioc/manuals/les/man/les.pdf |
Package for using R in Matlab: |
R-Package for identification of the optimal imputation method: |
R-Package for statistical analyses of zero-inflated data: |
R-Package for simulating benchmark data: |
R-Package for the analysis of hierarchical count data: |
Agent-based model for finding an optiomal COVID-19 surveillance strategie: |
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The benchmarking wiki also offers the opportunity to publish (possibly small or unpublished) own results.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