scde
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hms-dbmi
R package for analyzing single-cell RNA-seq data
Hello, First of all thank you for developing this tool. I have a question regarding the output table of scde. I can understand the columns related to Z score and...
When I run pagoda.pathway.wPCA() multiple times on the same input I get different results, even if I set the seed before each run of this function. How can I ensure...
Hi, pagoda.cluster.cells produces NA's and a subsequent error. I think the problem is in line 2646 of functions.R, which states: gw
Hi, I followed the instructions, successfully installed all the dependent packages but got following error when installing SCDE: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared...
R 3.2.5 Installing from devtools gives me this error: > Installing BiocParallel > '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD \ > INSTALL '/tmp/RtmpBv2SbE/devtools881174ee69a1/BiocParallel' \ > --library='/home/billylau/R/x86_64-pc-linux-gnu-library/3.2' --install-tests > >...
Multiple users have experienced errors when increasing the number of cores to > 1 https://groups.google.com/forum/#!topic/singlecellstats/Miwy1Jg6PRU https://groups.google.com/forum/#!topic/singlecellstats/ij2GWC1JLr0 The error may stem from updates to mclapply or bclapply.
In version 2.2.0 of the R package, the parameter `save.model.plots` to `knn.error.models` is unused and instead it saves plots only `if (length(vic) < length(ids)) {`. In R/functions.R (line 1264) this...
From Nikolas: "The last lines of the tutorial with the tSNE embedding don't quite work out of the box. You may want to substitute with the following: tSNE.pagoda
Previously had SVG exports. Recently changed to PNG for faster rendering to accommodate 1000s of cells. Provide both. This would also provide copyable gene names instead of a flattened render.
Undocumented code objects: ‘make.pagoda.app’ ‘o.ifm’ ‘pagoda.reduce.redundancy’ ‘pagoda.view.aspects’ ‘scde.edff’ Undocumented data sets: ‘o.ifm’ ‘scde.edff’ Undocumented arguments in documentation object 'pagoda.cluster.cells' ‘verbose’ ‘return.details’ Undocumented arguments in documentation object 'pagoda.reduce.loading.redundancy' ‘abs’ Documented arguments...