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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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Adding annotations #135

Open AteeqMKhaliq opened 4 years ago

AteeqMKhaliq commented 4 years ago

Hi, We have created singleR object without giving annotations txt file, can we add annotations for the cells to the singleR object without re-running the computationally intensive steps like fine.tune=T again? are they're a way to do this without re-running the following code again We have ~ 50000 Cells and two categories (Normal Vs Diseased)

singler_new <- CreateSinglerSeuratObject(counts = counts, project.name = '', species = "Human", annot= NULL, min.genes = 500, min.cells = 2, npca = 10, technology = "X10", citation = "", ref.list = list(), normalize.gene.length = F, variable.genes = "de", fine.tune = T, do.signatures = T, do.main.types = T, reduce.file.size = T, numCores = 8)

to this

singler_new <- CreateSinglerSeuratObject(counts = counts, project.name = '', species = "Human", annot= "colnames.count.txt", min.genes = 500, min.cells = 2, npca = 10, technology = "X10", citation = "", ref.list = list(), normalize.gene.length = F, variable.genes = "de", fine.tune = T, do.signatures = T, do.main.types = T, reduce.file.size = T, numCores = 4)

Regards, Jack

dviraran commented 4 years ago

Please post issues in https://github.com/LTLA/SingleR

Thanks, Dvir

AteeqMKhaliq commented 4 years ago

Hi Dvir, I have posted it on LTLA, it is very critical for us, Please help us to get a solution. It took us almost 9 days to finish the analysis and we don't want to re do it again. regards, Jack