Various tools developed in our group are available on GitHub.
CAP Severity Scores
Shiny app for the calculation of several CAP severity scores.
This Shiny app implements the calculation of several CAP (Community-Aquired-Pneumonia) severity scores for one or multiple patients based on user-updated data. The Shiny-App is integrated in the LHA (Leipzig Health Atlas) here.
CP
CP is an R package for conditional power calculation in survival time analysis considering cure fractions.
We derived conditional power formulae for the non-mixture exponential, the non-mixture Weibull, and the non-mixture Gamma models. Formulae were implemented in the R package CP which can be downloaded at CRAN. As an introduction, see the publication.
eQTL-Search
Shiny app for download and searching of summary statistics.
This Shiny app facilitates the download and searching of the summary statistics from "Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci" (https://doi.org/10.1093/hmg/ddv194). It is integrated in the LHA (Leipzig Health Atlas) here.
fcGENE
fcGENE is an open-source format converting tool for genotype data.
The tool is useful for preparing SNP data for genotype imputation analysis. fcGENE converts the Plink data format into input files required for a variety of imputation software packages such as MACH, IMPUTE, BEAGLE and BIMBAM. It also converts the output of these packages back to plink format.
Source files can be downloaded at SourceForge. As an introduction, see the publication.
HT12ProcessoR
Preprocessing ILLUMINA HT12v4 data intended for projects up to thousands of samples.
The R package preprocesses Illumina HT12v4 gene expression data including quality filtering, data transformation and normalisation and batch-effect removal as well as visualisation. It can be downloaded from GitHub.
KMWin
KMWin (Kaplan-Meier for Windows) is a convenient tool for graphical presentation of results from Kaplan-Meier survival time analysis.
The programme is based on the statistical software environment R and provides an easy to use graphical interface. Source files can be downloaded at SourceForge. As an introduction, see the publication.
Metabolite-Investigator
Shiny app for investigation of metabolite-covariate relationships.
The main goal is to provide a principled analysis workflow addressing specific issues of mass-spectrometry metabolite measurements in the context of testing in multiple studies with a high number of hypotheses. The source code of this app is available at GitHub. A detailed description of the methods used in the analysis as well as an application with data for 63 metabolites and 29 factors in three studies (N=16,222) is integrated in the LHA (Leipzig Health Atlas) here.
Ycasd
Ycasd (ycasd captures and scales data) is a simple tool for capturing and scaling data from graphical representations.
The tool can be used for retrieving data points from figures of electronically available or scanned publications for which no raw data is provided. Source files are accessible via SourceForge. For details, see the publication.