No particular installation is needed, just the files of this repository need to be downloaded.
In order to generate a project-specific HTML, that allows to query data, either genes or DEG lists, it needs to run the python scripts
GUI supported run
A user has to specific the needed files by choosing files from the Graphical User Inferface (starting biosankey.py). There a user can upload expression information, domain information or microbial information.
For demonstration purposes, we used the data from Morandi, Elena, et al. "Gene expression timeseries analysis of camptothecin effects in U87MG and DBTRG05 glioblastoma cell lines." Molecular cancer 7.1 (2008): 66. containing expression information at six different timepoints: 2h, 6h, 16h, 24h, 48h, and 72h.
We also added an use case (Use case 2) where we included OTU from Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, and Knight R. 2011. Moving pictures of the human microbiome. Genome Biol 12:R50. 10.1186/gb-2011-12-5-r50
Format of input data:
Genes divided in up and downregulated or abundances of genes or other entities (microbial species of a certain taxon, metabolites, ...)
It requires, that all timepoints of interest containing the genes and are also contained in the expression data lists. E.g. genes, that are upregulated at 16h and downregulated would be summarized in the file: '16h_down.dat'.
Picture export in high-quality
In order to provide publication-ready images, we suggest to use PhantomJs, which allows to make a screenshot of the current webseite. Link to PhantomJs
phantomjs-2.1.1-linux-i686/bin/phantomjs rasterize.js 'Use_case_combined.html' V1.png "100cm*80cm" 3 convert V1.png -trim V1x1.png
After the OTU Table has been added using the GUI and after clicking on the microbiome Button, the BioSankey plot opens and the taxonomic groups are shown.
Excel to tab export
In order to export Excelt o tsv, we recommend to use xlsx2tsv.
Questions and problems
If there are any issues and suggestions, please contact Alexander Platzer ( alexander.platzer AT univie.ac.at ) or Thomas Nussbaumer ( thomas.nussbaumer AT univie.ac.at )