Admin: Hervé Pagès
Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès
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Answer:
A: BiocCheck package size
... This question is about package development hence should be asked on the bioc-devel mailing list:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Thanks,
H. ...
written 3 hours ago by
Hervé Pagès ♦♦ 13k
2
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66
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... Hi,
A workaround is to perform your own merge e.g. with something like this:
```
library(S4Vectors)
x <- DataFrame(tx_id=letters[1:7], gene_id=c(3, 19, 4, 1, 1, 3, 1))
y <- DataFrame(gene_id=1:5, gene_name=LETTERS[1:5])
m <- match(x$gene_id, y$gene_id)
cbind(x, y[m, ])
# DataFrame with 7 r ...
written 3 days ago by
Hervé Pagès ♦♦ 13k
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... Please edit your post to make proper use of markdown so underscores and other important characters don't disappear. For example wrap file paths and R expressions in backquotes (`` ` ``) so we can see exactly what they look like and even copy/paste them in our own R sessions. This should give somethi ...
written 21 days ago by
Hervé Pagès ♦♦ 13k
0
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95
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... `sessionInfo()` please? Thanks ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
1
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... And FWIW here is the fast version of it:
```
trimFivePrimeSide <- function(gr, remove)
{
stopifnot(is(gr, "GenomicRanges"), is(remove, "GenomicRanges"))
mapping <- as(findOverlaps(gr, remove), "IntegerList")
new_start_on_plus_strand <- pmin(max(extractList(end(remove),
...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
0
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... FWIW you might also want to take a look at `Biostrings::replaceAt()`. It's lower level and more flexible than `BSgenome::injectSNPs()` (the former works on AAString/AAStringSet/DNAString/DNAStringSet objects while the later only works on a BSgenome object). ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
0
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... Hi,
So IIUC, for each gene you want the longest upstream region that is <= 2kb and does not overlap with any known CDS. Or, said otherwise, you want to minimally trim (on the 5' side) the upstream regions in `gnflanks` so that they are CDS-free. Note that this trimming will sometimes result in a ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
3
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... Hi,
Please be aware that some familiarity with R is highly recommended before you can efficiently use Bioconductor.
It's not clear to me whether you want to extract the upstream and downstream _regions_ (i.e. their coordinates with respect to the reference genome) or the _genomic sequences_ (DNA) ...
written 7 weeks ago by
Hervé Pagès ♦♦ 13k
0
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210
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... BTW this change was finally announced recently on the Genome Browser's blog:
http://genome.ucsc.edu/blog/patches/
and on their mailing list:
https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome-announce/oMMnhnPr6gg
The hg38 gateway page still doesn't say what assembly the hg38 tracks ar ...
written 7 weeks ago by
Hervé Pagès ♦♦ 13k
1
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... Should be fixed in GenomeInfoDb 1.19.2 (devel, see commit [here](
https://github.com/Bioconductor/GenomeInfoDb/commit/18c1056adb2304b0e194df31acbf061c6f6ec04b)) and 1.18.2 (release). These new versions won't show up on the build reports ([devel](https://bioconductor.org/checkResults/devel/bioc-LATES ...
written 10 weeks ago by
Hervé Pagès ♦♦ 13k
Latest awards to Hervé Pagès
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3 months ago,
created an answer with at least 3 up-votes.
For A: Calling coverage on GRanges object yields small negative values
Scholar
3 months ago,
created an answer that has been accepted.
For A: coverage() output SimpleRleList cannot be converted to GRanges
Good Answer
4 months ago,
created an answer that was upvoted at least 5 times.
For A: how to extract "Gene type" from org.Mm.eg.db?
Appreciated
4 months ago,
created a post with more than 5 votes.
For C: Error in GRanges: could not find symbol "recursive" in environment of the generi
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7 months ago,
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For unique, duplicated, order, etc... on a GRanges object
Popular Question
7 months ago,
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For BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Scholar
7 months ago,
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For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Extracting Coordinates of startcodon from Grangeslist
Teacher
7 months ago,
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For A: Calling coverage on GRanges object yields small negative values
Popular Question
7 months ago,
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For how to obtain base counts from BAM file at specific genomic coordinates
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7 months ago,
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For A: Extracting Coordinates of startcodon from Grangeslist
Teacher
8 months ago,
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For A: Extracting Coordinates of startcodon from Grangeslist
Scholar
11 months ago,
created an answer that has been accepted.
For A: coverage() output SimpleRleList cannot be converted to GRanges
Scholar
11 months ago,
created an answer that has been accepted.
For A: Extracting Coordinates of startcodon from Grangeslist
Scholar
11 months ago,
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For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar
11 months ago,
created an answer that has been accepted.
For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Extracting Coordinates of startcodon from Grangeslist
Teacher
22 months ago,
created an answer with at least 3 up-votes.
For A: extract subsequence(s) from DNAStringSet with getSeq
Teacher
22 months ago,
created an answer with at least 3 up-votes.
For A: about setdiff() and meta-information in GRanges
Teacher
22 months ago,
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For A: Extracting Coordinates of startcodon from Grangeslist
Teacher
22 months ago,
created an answer with at least 3 up-votes.
For A: How do I merge a list of GRanges?
Teacher
22 months ago,
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For A: Error when running "locateVariants" function in "VariantAnnotation" package
Teacher
22 months ago,
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For A: overlapsAny for elements in GRangesList
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22 months ago,
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For C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
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22 months ago,
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For C: Error in GRanges: could not find symbol "recursive" in environment of the generi
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