ngs_tools issueshttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues2021-04-08T13:38:56Zhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/103gsea: fixing expression explorer2021-04-08T13:38:56Zgohrgsea: fixing expression explorerThe EE uses the package shinyjqui. This package has changed data structures which caused the EE to not work properly for the most recent version 0.4.0 of this package. Searching + adapting EE to make it run with all versions of shinyjqui...The EE uses the package shinyjqui. This package has changed data structures which caused the EE to not work properly for the most recent version 0.4.0 of this package. Searching + adapting EE to make it run with all versions of shinyjqui until v0.4.0. I've added expression_explorer.yml with a minimal Conda env to run the EE. On top, I've change the EE to not depend anymore on devtools and additional SCF internal scripts which includes to load libraries with library statements rather then load_pack statements.gohrgohrhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/102gsea: improvement of description2021-04-08T13:39:07Zgohrgsea: improvement of descriptionThe current description is misleading as of where up- and down-regulated genes are in the list of sorted analyzed genes. It's true that genes are sorted according to diff. expression from down-regulated to up-regulated genes but the GSEA...The current description is misleading as of where up- and down-regulated genes are in the list of sorted analyzed genes. It's true that genes are sorted according to diff. expression from down-regulated to up-regulated genes but the GSEA inverses this list and output results (plots) will have the up-regulated genes at the beginning and the down-regulated genes at the end.
I've changed the GSEA description to be more clear on this aspect. I also shortened it to be more precise.gohrgohr