User: jbalberge

gravatar for jbalberge
jbalberge80
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France/Nantes
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jbalberge
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4 days, 3 hours ago
Joined:
1 year, 7 months ago
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Posts by jbalberge

<prev • 9 results • page 1 of 1 • next >
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Answer: A: how to produce Dot plots in R
... Assuming you're analyzing single-cell RNA seq data, you can use the DotPlot function from Seurat: DotPlot(object = pbmc, genes.plot = features.plot, plot.legend = TRUE) thanks to https://satijalab.org/seurat/visualization_vignette.html ...
written 4 months ago by jbalberge80
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Comment: C: Cannot run or build KING on Mac OS X
... Great! Thanks for the updates! ...
written 7 months ago by jbalberge80
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Comment: C: Cannot run or build KING on Mac OS X
... My bad, building c++ code with the Open MP lib on Mac OS X seems quite hard. Let's go back to the compiled version. I managed to have it work after setting the dyld library path brew install gcc brew link gcc export DYLD_LIBRARY_PATH=/usr/local/lib/gcc/8/:$DYLD_LIBRARY_PATH ./king - ...
written 7 months ago by jbalberge80
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Answer: A: Cannot run KING on Mac OS X
... KING was probably built with gcc 6.x and is looking for a gcc 6 library. Try build your own KING with the C++ source code with http://people.virginia.edu/~wc9c/KING/KINGcode.tar.gz as mentioned in http://people.virginia.edu/~wc9c/KING/Download.htm cd Downloads/KINGcode/ c++ -lm -lz -O2 -fop ...
written 7 months ago by jbalberge80
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Comment: C: Storing a gene expression matrix in a matrix.mtx
... What do you mean correct? Isn't it correct though? Should you have any non-integer value in your matrix, it would be stored differently (real, complex) by the R library. Could be that the matrix writer from your tutorial is not the same. This line `13406 1562 6512772` tells the matrix reader that yo ...
written 7 months ago by jbalberge80
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Comment: C: Storing a gene expression matrix in a matrix.mtx
... Replace `gbm` (=gene-barcode matrix) by `all.counts` : sparse.all.counts <- Matrix(all.counts , sparse = T ) # save all.counts as a sparse matrix head(sparse.all.counts) writeMM(obj = sparse.all.counts, file="matrix.mtx") # write the sparse matrix in the matrix.mtx file ...
written 7 months ago by jbalberge80
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Answer: A: Storing a gene expression matrix in a matrix.mtx
... Hi! Use the Matrix library to create and write a sparse matrix: library(Matrix) # generate single-cell RNA seq data gbm <- replicate(10, rpois(10, 1)) rownames(gbm) <- paste0("gene_", 1:nrow(gbm)) colnames(gbm) <- paste0("cell_",1:ncol(gbm)) # save sparse ...
written 7 months ago by jbalberge80
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Comment: C: Question chip enrichment
... It seems that Gencode / RefSeq annotation files downloaded from UCSC in GTF format don't contain transcript and gene entries. I got the same error with gtf files downloaded on UCSC. Problem solved by downloading gtf files from Gencode instead. > library(data.table) > hg38.gtf <- da ...
written 7 months ago by jbalberge80
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Answer: A: Searching wgs (whole genome shotgun) database with biopython
... The list of WGS databases can be retrieved with taxids2wgs.pl: ftp://ftp.ncbi.nlm.nih.gov/blast/WGS_TOOLS $ perl taxid2wgs.pl -url_api_ready 487 > wgs_dbs_tax_487 It contains the WGS accesses WGS_VDB://MTKJ01 WGS_VDB://MTKM01 WGS_VDB://LXLB01 WGS_VDB://LXLA01 WGS_VDB:// ...
written 19 months ago by jbalberge80

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Scholar 7 months ago, created an answer that has been accepted. For A: Storing a gene expression matrix in a matrix.mtx

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