The compute 5 pipeline from MOLGENIS
was used to process the data.
This pipeline contains several other features that were used to obtain results for BRAIN-sat.
Aligning was done with HISAT2
was used to perform a quality check on obtained datasets.
Several preprocessing steps were performed with Picard
was used to obtain the counts for the datasets.
The interactive analyses are done with R. The filtering of low expression genes is done with the use of DAFS: a data-adaptive flag method
is used to generate the differential gene expression lists and to obtain the quantitative gene information, and scatterD3
was used to create the interactive QE bargraphs.
The set-up of MOLGENIS
The sorting of the table content was done with the use of sorttable
was used in order to develop the interactive images of the QE data and the implementation of html2canvas
make sure that these images can be downloaded.
was used to generate the interactive images of the single cell data and the differential expression vulcano scatterplot of the bulk RNA data.
- Holtman et al. (2015). Glia Open Access Database (GOAD): A comprehensive gene expression encyclopedia of glia cells in health and disease.
Glia 63:1495–1506 doi: 10.1002/glia.22810 Pubmed
We would like to thank the following people for the contribution of BRAIN-SAT:
For supervising students from the Hanzehogeschool, we would like to thank M.A. Noback and R. Wedema.
S. N. Dubbelaar for the creation of the BRAIN-SAT logo.