ngs_tools issueshttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues2017-07-08T23:44:42Zhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/8create tool to create igv session file list of bam files2017-07-08T23:44:42Zbrandlbrandl@mpi-cbg.decreate tool to create igv session file list of bam files@lakshman fyi https://github.com/igvteam/igv/issues/234@lakshman fyi https://github.com/igvteam/igv/issues/234https://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/7finish panther enrichment and reintegrate into cp_enrichment.R2020-02-20T16:06:56Zbrandlbrandl@mpi-cbg.definish panther enrichment and reintegrate into cp_enrichment.Rsee
/Volumes/furiosa/bioinfo/scripts/ngs_tools/dev/common/panther_enrichment.R
/Volumes/furiosa/bioinfo/scripts/ngs_tools/dev/common/cp_enrichment.Rsee
/Volumes/furiosa/bioinfo/scripts/ngs_tools/dev/common/panther_enrichment.R
/Volumes/furiosa/bioinfo/scripts/ngs_tools/dev/common/cp_enrichment.Rhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/6Add pcr duplication analysis for rna-seq workflow2017-11-09T15:39:52Zbrandlbrandl@mpi-cbg.deAdd pcr duplication analysis for rna-seq workflowhttps://www.bioconductor.org/packages/release/bioc/html/dupRadar.html
@lakshman what do you thinkhttps://www.bioconductor.org/packages/release/bioc/html/dupRadar.html
@lakshman what do you thinkhttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/5add frip statistic to cs-workflow2019-03-07T15:17:04Zbrandlbrandl@mpi-cbg.deadd frip statistic to cs-workflowa standard measure of the signal-to-noise ratio is the FRiP (fraction of reads in peaks),
@lakshman what do you think a about a more standardized chipseq-workflow?a standard measure of the signal-to-noise ratio is the FRiP (fraction of reads in peaks),
@lakshman what do you think a about a more standardized chipseq-workflow?https://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/4Add groupGo to cp_enrichment2017-11-09T15:40:26Zbrandlbrandl@mpi-cbg.deAdd groupGo to cp_enrichmentlevel=7 seem reasonable.
@lakshman just fyi
also add median fc / score to make terms more informative. (to illucidate which terms that changed)level=7 seem reasonable.
@lakshman just fyi
also add median fc / score to make terms more informative. (to illucidate which terms that changed)brandlbrandl@mpi-cbg.debrandlbrandl@mpi-cbg.dehttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/3couldn't export the bitr function in clusterprofiler2017-07-08T23:44:42Zlakshmancouldn't export the bitr function in clusterprofilerany ideas on the problem below?
https://git.mpi-cbg.de/bioinfo/ngs_tools/blob/master/common/cp_enrichment.R#L131
![image](/uploads/bec7b19bc4b56af5e1b79dc65c6edfd7/image.png)
any ideas on the problem below?
https://git.mpi-cbg.de/bioinfo/ngs_tools/blob/master/common/cp_enrichment.R#L131
![image](/uploads/bec7b19bc4b56af5e1b79dc65c6edfd7/image.png)
brandlbrandl@mpi-cbg.debrandlbrandl@mpi-cbg.dehttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/2error in the plotDispEsts()2017-07-08T23:44:42Zlakshmanerror in the plotDispEsts()https://git.mpi-cbg.de/bioinfo/ngs_tools/blob/master/dge_workflow/featcounts_deseq.R#L143
![image](/uploads/332f69d55dfa57f460803a34d2d4f598/image.png)
https://git.mpi-cbg.de/bioinfo/ngs_tools/blob/master/dge_workflow/featcounts_deseq.R#L143
![image](/uploads/332f69d55dfa57f460803a34d2d4f598/image.png)
brandlbrandl@mpi-cbg.debrandlbrandl@mpi-cbg.dehttps://git.mpi-cbg.de/bioinfo/ngs_tools/-/issues/1make sure that exported tables contain double-normalized counts and not just ...2019-02-12T10:35:31Zbrandlbrandl@mpi-cbg.demake sure that exported tables contain double-normalized counts and not just size-normalized onesbrandlbrandl@mpi-cbg.debrandlbrandl@mpi-cbg.de