sc-TissueMapper_Pr issueshttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues2018-11-03T01:07:25-05:00https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/23Pd DEG not have all OE pops in comparisons!2018-11-03T01:07:25-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduPd DEG not have all OE pops in comparisons!Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu2018-11-05https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/22Remove depreciated scripts2018-10-01T13:36:20-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduRemove depreciated scriptsGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/21Add Surface/Nucleus predictor2019-08-13T00:06:41-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd Surface/Nucleus predictorGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/20Make unique names for QC plots2019-08-13T00:06:49-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMake unique names for QC plotsIn multiple dataset loadIn multiple dataset loadGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/19Fix CCA VlnPlot2018-06-18T08:10:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix CCA VlnPlotChange to:
plot <- VlnPlot...
plot(plot)Change to:
plot <- VlnPlot...
plot(plot)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/18Alter PCA cutoff2018-06-11T16:34:55-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAlter PCA cutoffUse lowest local minima AFTER the global maximaUse lowest local minima AFTER the global maximaGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/17Integrate Jackstraw with multi-core parallel processing2018-06-11T16:35:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduIntegrate Jackstraw with multi-core parallel processingGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/16Fix QuSAGE tSNE ouput filenames2018-04-12T14:33:44-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix QuSAGE tSNE ouput filenamesEpi overwrite subpop ?
St name merge pop "SubPop" ?Epi overwrite subpop ?
St name merge pop "SubPop" ?Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/15Test clusterProfiler in lieu of QuSAGE2019-08-13T00:05:22-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduTest clusterProfiler in lieu of QuSAGEGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/14Reintegrate nuclear/surface marker prediction into DEG generation2018-04-09T20:01:29-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduReintegrate nuclear/surface marker prediction into DEG generationGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/13Allow Epi/St SubClust Merge to have different resolutions2018-04-09T12:53:23-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAllow Epi/St SubClust Merge to have different resolutionsGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/12LineageSubClust (Epi+St) res tSNE's put in global directory when NoStress ana...2018-04-09T12:59:00-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduLineageSubClust (Epi+St) res tSNE's put in global directory when NoStress analysis selectedGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/11Integrate new suggested technique for large data handling from seurat2018-04-16T10:28:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduIntegrate new suggested technique for large data handling from seuratGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/10Recreate CI TestData Create r.script2018-03-30T00:51:31-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduRecreate CI TestData Create r.scriptGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/9Change r.scripts to functions2018-06-11T16:35:23-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduChange r.scripts to functionsGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/8Make bash.scripts take project from command line and pass to Rscript opt2019-08-13T00:06:56-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMake bash.scripts take project from command line and pass to Rscript opt"$1""$1"Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/7Add code to reorder cells in tSNE (especially in NE)2018-04-09T11:22:57-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd code to reorder cells in tSNE (especially in NE)Modify from:
```
ss10x.DPrPz <- SetAllIdent(object = ss10x.DPrPz, id = "samples")
Background <- NULL
for (i in c('D17PrPzF_FMSt','D17PrPzF_LE','D17PrPzF_OE','D17PrPzF_Via','D17PrTzF_Via')){
Background <- c(Background,names(ss10x.DPrPz@...Modify from:
```
ss10x.DPrPz <- SetAllIdent(object = ss10x.DPrPz, id = "samples")
Background <- NULL
for (i in c('D17PrPzF_FMSt','D17PrPzF_LE','D17PrPzF_OE','D17PrPzF_Via','D17PrTzF_Via')){
Background <- c(Background,names(ss10x.DPrPz@ident[ss10x.DPrPz@ident==i]))
}
ss10x.DPrPz <- SetIdent(ss10x.DPrPz, Background,'Background')
ss10x.DPrPz@ident <- factor(ss10x.DPrPz@ident,levels=c("D17PrPzF_BE","Background"))
ss10x.DPrPz.test@data <- ss10x.DPrPz@data[,c(Background,colnames(ss10x.DPrPz.test@data)[!colnames(ss10x.DPrPz@data) %in% Background])]
```Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/6Fix OE1/2 order in dot plot on sc_DEG.R2018-06-17T17:41:05-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix OE1/2 order in dot plot on sc_DEG.RAgain?Again?Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/5Fix NE display2018-05-14T09:11:46-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix NE displayPC1 (NE Score) polarity
PCS_NE.Epi.Group.eps NE incorrectly labeledPC1 (NE Score) polarity
PCS_NE.Epi.Group.eps NE incorrectly labeledGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/4Allow DEG and Table scripts to run without NE ID2018-04-09T13:48:35-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAllow DEG and Table scripts to run without NE IDGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu