Moderator: Michael Lawrence

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Posts by Michael Lawrence

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Comment: C: Efficient counting of nucleotide changes in short-reads
... Sorry I will edit my answer. ...
written 1 day ago by Michael Lawrence10k
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Answer: A: Efficient counting of nucleotide changes in short-reads
... To get tallies by read position, you could try VariantTools::tallyVariants() and its read_pos_breaks parameter. Set it to e.g. 0:72 to get a tally for every read position, by every position in the genome. Then you'll need to colSums() those columns in the result. ...
written 2 days ago by Michael Lawrence10k
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Comment: C: How is it possible to override the constructor of the GRanges class?
... Maybe you are looking for metadata(temp)$name <- "ABC"? ...
written 3 days ago by Michael Lawrence10k
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Comment: C: ggbio won't plot ideogram in R version 3.3.1, ggplot2 version 3.1.0
... Unfortunately ggbio is only supported on R 3.5.   ...
written 9 days ago by Michael Lawrence10k
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Answer: A: Subset bam file in R
... You could use the rtracklayer export() function. But I think you really want Rsamtools::filterBam() in this case. ...
written 10 days ago by Michael Lawrence10k
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Comment: C: Install rtracklayer with the Error undefined symbol: OPENSSL_init_ssl (system Ce
... If you have root, you could probably try updating your openssl to 1.1.0 or above. But if you can't set an environment variable, that might be a tall order. ...
written 11 days ago by Michael Lawrence10k
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Comment: C: Install rtracklayer with the Error undefined symbol: OPENSSL_init_ssl (system Ce
... Since you're using CentOS, I wonder if you're using R in an enterprise environment, where you might have system support staff available to help you? ...
written 12 days ago by Michael Lawrence10k
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Comment: C: Install rtracklayer with the Error undefined symbol: OPENSSL_init_ssl (system Ce
... I wouldn't do any renaming of files. You're going to have to figure out the versions of your openssl headers and libraries, and make sure that you're using the same version for both by setting environment variables as described previously. ...
written 12 days ago by Michael Lawrence10k
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Comment: C: Install rtracklayer with the Error undefined symbol: OPENSSL_init_ssl (system Ce
... It's strange how the actual building of the package is not in the log. Are you omitting that? Probably what's happening here is that the build process is finding openssl >=1.1.0 headers, which map SSL_library_init() to OPENSSL_init_ssl(), but the runtime linker is finding an older openssl lib (& ...
written 12 days ago by Michael Lawrence10k
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Answer: A: rtracklayer::Problem with export.bw of GRanges object created by unlisted after
... If the lift over process produces overlapping ranges, then you'll need to resolve those somehow before exporting. How you do that depends on your overall goals/question. ...
written 17 days ago by Michael Lawrence10k

Latest awards to Michael Lawrence

Scholar 6 weeks ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 6 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 6 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 17 months ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Scholar 17 months ago, created an answer that has been accepted. For A: filtering VCF files
Scholar 17 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 17 months ago, created an answer that has been accepted. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 17 months ago, created an answer that has been accepted. For A: Genomic Ranges findOverlaps by sample
Scholar 17 months ago, created an answer that has been accepted. For A: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 17 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 17 months ago, created an answer that has been accepted. For A: closest-features equivalent in Bioconductor for finding closest gene(s)
Scholar 17 months ago, created an answer that has been accepted. For A: reduce function after combining 2 GRanges objects from cn.mops output
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: filtering VCF files
Scholar 17 months ago, created an answer that has been accepted. For A: issue renaming seqnames in genomic ranges
Scholar 17 months ago, created an answer that has been accepted. For A: does import.bw with the selection argument take into account strand?
Scholar 17 months ago, created an answer that has been accepted. For A: VariantAnnotation as.vranges with asterisk in ALT field
Scholar 17 months ago, created an answer that has been accepted. For A: Group GRanges and keep metadata
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: What is the proper way to modify mcols of a GRanges inside a GRangesList?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: annotate GRanges with upstream or downstream nearest gene

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