Moderator: Michael Lawrence

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Email:
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Posts by Michael Lawrence

<prev • 1,354 results • page 1 of 136 • next >
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Answer: A: ggbio tracks not aligned when legend present in one track
... Thanks for the report. The original author of ggbio abandoned the project many years ago. At this point, I can make minor fixes but this is probably going beyond that. ...
written 8 days ago by Michael Lawrence11k
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Comment: C: An error while finding pintersect()
... Your version of R/Bioconductor is a few years old and no longer supported. Please update and see if the problem persists. ...
written 21 days ago by Michael Lawrence11k
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Answer: A: rtracklayer::export empty score
... The score column needs to be named "score". ...
written 22 days ago by Michael Lawrence11k
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Comment: C: How to query a base along an aligned read by genomic position?
... The "molecule" in this case is the sequence read. ...
written 5 weeks ago by Michael Lawrence11k
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Comment: C: How to query a base along an aligned read by genomic position?
... `readGAlignments()` accepts a ScanBamParam via `param=`. If the sequence and qualities are in the "what" they will be included in the `mcols()`. The names are required since the mapped return value needs to use the read identifiers as its seqnames. ...
written 6 weeks ago by Michael Lawrence11k
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Comment: C: Annotating GRanges with TxDb gene models using plyranges
... I don't know whether there is any equivalent in the dplyr world, but it might be useful to have a function that rather than expand the left object instead splits the right object and attaches it as a new metadata column. I was unable to load the data file in your example (possible corruption?), but ...
written 8 weeks ago by Michael Lawrence11k
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Answer: A: Coverage function assigns wrong weights for gapped alignments
... Seems like a bug in `coverage,GRangesList()`, because it should automatically expand the weights. For a relatively simple speed up, consider: ``` grl <- grglist(reads) weight <- mcols(reads)$weight[togroup(PartitioningByEnd(grl))] coverage(grl, weight) ``` ...
written 9 weeks ago by Michael Lawrence11k
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Comment: C: Can GenomicRanges findOverlaps ignore seqnames?
... Would you please provide more details on the use case? ...
written 9 weeks ago by Michael Lawrence11k
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Comment: C: Best way to subset one IRanges by list of IRanges
... I see, in that case I'm not sure if that is really a subset operation. It's more like `extractList()` except by overlap. ...
written 11 weeks ago by Michael Lawrence11k
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Comment: C: Best way to subset one IRanges by list of IRanges
... Would you be interested in contributing a `subsetByOverlaps()` method? Btw, I think you do need to reverse the arguments from your initial example, i.e., `subsetByOverlaps(slist, query)`. The simplest thing to do is `unlist(slist)`, perform the subset, then reform the list, which would be the slight ...
written 11 weeks ago by Michael Lawrence11k

Latest awards to Michael Lawrence

Scholar 5 months ago, created an answer that has been accepted. For A: Extract metadata from GRanges object for every genomic coordinate
Scholar 11 months ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 11 months ago, created an answer that has been accepted. For A: How can I create a GmapGenome that doesn't start at index 1?
Popular Question 11 months ago, created a question with more than 1,000 views. For Job Opening: Computational Biologist @ Genentech Bioinformatics
Scholar 11 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Scholar 11 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to use GenomicRanges to find overlaps by percentage covered of interval
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Importing Gene Symbols with makeTxDbFromGFF
Scholar 11 months ago, created an answer that has been accepted. For A: How to use GenomicRanges to find overlaps by percentage covered of interval
Scholar 11 months ago, created an answer that has been accepted. For A: DataFrame after splitting and back
Popular Question 11 months ago, created a question with more than 1,000 views. For views on Rle using GRanges object
Appreciated 11 months ago, created a post with more than 5 votes. For A: How to use GenomicRanges to find overlaps by percentage covered of interval
Scholar 11 months ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Scholar 11 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Scholar 13 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Scholar 18 months ago, created an answer that has been accepted. For A: Detecting Overlaps within Grange Object
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: trying to annotate overlaps with external file information
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: setdiff for GenomicRanges
Scholar 18 months ago, created an answer that has been accepted. For A: Features within 2kb window, but with resampling
Scholar 2.5 years ago, created an answer that has been accepted. For A: trying to annotate overlaps with external file information
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: unlist a exons GRangeslist object and add a gene name column
Scholar 2.5 years ago, created an answer that has been accepted. For A: Subset GRanges object into new object
Scholar 2.5 years ago, created an answer that has been accepted. For A: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?

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