Then, for manipulating these files, you should refer to their tutorial (it's beyond my skills and the scope of your question). Matrix H5I_DATASET 6667 x 24421 H5T_FLOAT Name obj_type dataset.dims dataset.type_class Lfile = connect(filename = "SCG71.loom", mode = "r+")Īttributes: creation_date, chunks, velocyto._version_, velocyto.logic, version "SCG71:AAACAAACAGCAGAAC" "SCG71:AAACAAACTTTGGGAG"Īfter that, I don't know what to do with that but I think your issue of importing a datafile is because you don't have the right package to open it.Īlternatively, you can also install the package loomR and then enter: library(loomR) "SCG71:AAACGATCCTACTTGT" "SCG71:AAACACTACGTAGAAG" "SCG71:AAACACGGCATCGCAG" You can then load some data > scle$CellID Metadata(4): chunks creation_date velocyto._version_ velocyto.logicĪssays(4): matrix ambiguous spliced unspliced On my computer, once I get it install, I was able to load your SCG71.loom file using: library(LoomExperiment) On bioconductor, you can also find LoomExperiment. $ ambiguous:Formal class 'dgCMatrix' with 6 slots ![]() ![]() $ unspliced:Formal class 'dgCMatrix' with 6 slots analysis software R and R Studio Statistical computing and graphics software. $ : chr "SCG71:AAACGATCCTACTTGT" "SCG71:AAACACTACGTAGAAG" "SCG71:AAACACGGCATCGCAG" "SCG71:AAACAAACAGCAGAAC". Adobe Creative Cloud Graphic design and video editing software by Adobe. $ spliced :Formal class 'dgCMatrix' with 6 slots loom file but on the velocyto.R tutorial, it is specified to do the following: library(velocyto.R) ![]() I'm not very familiar with this kind of of. loom file that can be open using the velocyto.R package. The file that you are trying to import is not a velocyto file but a. I'm not sure that your issues is from RStudio cloud but more about how you are trying to open the file.
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