ngs_tools issueshttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues2020-09-15T15:13:36Zhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/95gsea: bug, in extra sets the first line is being read as header2020-09-15T15:13:36Zdominguegsea: bug, in extra sets the first line is being read as headerThis is leads to one set missing from the analysis.This is leads to one set missing from the analysis.dominguedominguehttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/96gsea: generate results for each contrast2020-09-23T12:06:53Zdominguegsea: generate results for each contrastRight now all genes are taken into account because I had only single contrast experiment but this is not always the caseRight now all genes are taken into account because I had only single contrast experiment but this is not always the casedominguedominguehttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/98Gene enrichment: script selects random genes if list too large2020-10-07T14:53:05ZdomingueGene enrichment: script selects random genes if list too largeThe `cp_enr` function randomly samples genes if the list is larger than 1500 ([this bit](https://git.mpi-cbg.de/bioinfo/ngs_tools/-/blob/master/common/cp_utils.R#L123-125)).
Replace this function in the script until we start using `core...The `cp_enr` function randomly samples genes if the list is larger than 1500 ([this bit](https://git.mpi-cbg.de/bioinfo/ngs_tools/-/blob/master/common/cp_utils.R#L123-125)).
Replace this function in the script until we start using `corescf` [package](https://git.mpi-cbg.de/scicomp/bioinfo_team/corescf/)dominguedominguehttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/99gsea: better description2020-11-19T15:10:43Zdominguegsea: better descriptionI got feedback that the plots are not very intuitive. We need to add better explanations to the report.I got feedback that the plots are not very intuitive. We need to add better explanations to the report.dominguedominguehttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/100exDesign: numeric vs categorical variables and shrinkage method2021-02-23T07:51:33ZgohrexDesign: numeric vs categorical variables and shrinkage method- DESeq2 treats numeric experimental variables as numeric variables, not as discrete variables
- hence: all discrete variables should have values that are not numbers, e.g. litter1, litter, litter3 instead of 1, 2, 3
- DESeq2: one should...- DESeq2 treats numeric experimental variables as numeric variables, not as discrete variables
- hence: all discrete variables should have values that are not numbers, e.g. litter1, litter, litter3 instead of 1, 2, 3
- DESeq2: one should go through these steps:
1. contrast_oe <- c("sampletype", "MOV10_overexpression", "control")
2. res_tableOE_unshrunken <- results(dds, contrast=contrast_oe, alpha = 0.05)
3. res_tableOE <- lfcShrink(dds, contrast=contrast_oe, res=res_tableOE_unshrunken)
This allows to use other approaches for shrinking the logFC than the DEQeq standard approach See:
> What you observe is consistent with what we see in testing on the benchmarking data and on simulation data.
> If you just compare method="normal" to method="apeglm" or "ashr", the differences you are likely to see is
> that normal will shrink large effects even if they have high precision (so shrinking too much) and allow
> small effects to float around 0, while apeglm/ashr will not shrink the precise, large effects much at all and > the small effects which are indistinguishable from 0 will be shrunk to 0.
Papers show that these other two approaches are more effective.gohrgohrhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/101GSEA: improve color code of KEGG pathways2021-03-23T15:34:26ZgohrGSEA: improve color code of KEGG pathwaysKEGG pathways are overlayed with a color code that should represent differential gene expression. This code is flawed by the fact that some boxes/entities are associated with several genes and the abs.max over genes was color encoded wit...KEGG pathways are overlayed with a color code that should represent differential gene expression. This code is flawed by the fact that some boxes/entities are associated with several genes and the abs.max over genes was color encoded without information on the fact that it's several genes and which expression of which gene is displayed by color. The new version of cp_enrichment improves on this and now it makes clear
i) if there are several genes associated to a box/entity
ii) what is the diff. expression of all these genes
iii) color codes these diff. expressions in a coherent way so user can interpret the color codes.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.gohrgohrhttps://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.gohrgohr