sc-TissueMapper_Pr issueshttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues2018-03-27T18:51:17-05:00https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/1Add opt for no dowsampling in sc_PC.Score.Stress.R2018-03-27T18:51:17-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd opt for no dowsampling in sc_PC.Score.Stress.RSame as QuSAGESSame as QuSAGESGervaise 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/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/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/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.eduhttps://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/-/issues/2Prevent error if anchor gene doesn't exist in data2018-04-09T15:46:18-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduPrevent error if anchor gene doesn't exist in dataPC.ScorePC.ScoreGervaise 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/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/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/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/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/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/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/3Prevent error if NE fail because no NE2018-06-17T17:41:14-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduPrevent error if NE fail because no NEIn case where no NE, NE detection will assign large pop incorrectly and eventually cause an errorIn case where no NE, NE detection will assign large pop incorrectly and eventually cause an errorGervaise 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/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/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/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.edu