Admin: Hervé Pagès

gravatar for Hervé Pagès
Hervé Pagès ♦♦ 13k
Reputation:
12,660
Status:
Trusted
Location:
United States
Last seen:
1 day, 21 hours ago
Joined:
12 years, 2 months ago
Email:
h*****@fhcrc.org

Posts by Hervé Pagès

<prev • 1,552 results • page 1 of 156 • next >
0
votes
1
answers
81
views
1
answers
Comment: C: Is there a way to tell biocLite() to install a Bioconductor package only if it i
... FWIW setdiff(listOfBiocPackages, rownames(installed.packages())) does the same but is clearer and less typing than listOfBiocPackages[ which( !listOfBiocPackages %in% rownames(installed.packages()) ) ] H. ...
written 4 days ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
91
views
1
answers
Answer: A: coverage() output SimpleRleList cannot be converted to GRanges
... Hi Xiaotong, Thanks for reporting this. Not sure what "incompatibility between the new IRanges and GenomicRanges packages" you are talking about. To me, it looks like this happens when some list elements in the RleList object representing the coverage have length 0: library(GenomicRanges) cov0 ...
written 4 days ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
99
views
1
answers
Comment: C: How to find multiple overlaps with pairwiseAlignment()?
... Yes, the code I provided only works if there are only 2 overlapping regions that match with no indels (but mismatches should be ok). I'm afraid generalizing it to support N overlapping regions could get quite complicated... Cheers,   H. ...
written 12 days ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
71
views
1
answers
Answer: A: Unexpected behavior in Biostrings::pairwiseAlignment
... Hi, Note that by default pairwiseAlignments() performs global alignments so in your example the aligned subject is expected to be "--------", not "GATCGATC". Let's use a 1-letter subject: > pa1 <- pairwiseAlignment("GATCGATC", "T") # global > writePairwiseAlignments(pa1) ############### ...
written 12 days ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
129
views
1
answers
Answer: A: Error with makeTxDbFromBiomart in GenomicFeatures package
... Hi Simon, I can reproduce this with the current release version of GenomicFeatures (1.36.2). I tried with various datasets (ddiscoideum_eg_gene, tgondii_eg_gene, pvivax_eg_gene) and all of them gave me the same error that you got. This is actually easy to reproduce with a simple biomaRt query: li ...
written 16 days ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
99
views
1
answers
Answer: A: How to find multiple overlaps with pairwiseAlignment()?
... Hi Katarzyna, I think that you need to perform a local alignment for this (type="local"). Also it looks like you'll get best results by specifying gapExtension=0: library(Biostrings) dna1 <-   DNAString("NNNNNNATCGTTAAGCCCNNNNNTAGCAAAGGTAAANNNNN") dna2 <-   DNAString("++ATCGTTAAGCCC++++ ...
written 23 days ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
95
views
1
answers
Comment: C: Future plans for the new GPos class
... This is fixed in GenomicRanges 1.31.12 (BioC devel only):   https://github.com/Bioconductor/GenomicRanges/commit/27e6939c025029e56ed7dea9e9217dfe06278383 Should become available to BioC devel users via biocLite() in about 24 hours. Cheers, H. ...
written 23 days ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
127
views
1
answers
Comment: C: Query with Biostrings pairwise alignment output positon
... The man page for writePairwiseAlignments even contain the following example: ## -------------------------------------------------------------- ## C. REPRODUCING THE ALIGNMENT SHOWN AT ## http://emboss.sourceforge.net/docs/themes/alnformats/align.pair ## ----------------------------------------- ...
written 25 days ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
127
views
1
answers
Comment: C: Query with Biostrings pairwise alignment output positon
... Did you consult ?writePairwiseAlignments as I suggested? It explains the relationship between Biostrings' gapOpening/gapExtension and Emboss needle's Gap_penalty/Extend_penalty, and gives the formula to go from the latter to the former: Gap_penalty = gapOpening + gapExtension Extend_penalt ...
written 25 days ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
95
views
1
answers
Answer: A: Future plans for the new GPos class
... Hi, Thanks for letting us know about coverage() being broken on GPos objects. Will fix this. No particular plans for these objects except that at some point we're planning to support long GPos objects (i.e. objects that contain more than 2^31-1 positions). GPos is not being actively worked on anymo ...
written 4 weeks ago by Hervé Pagès ♦♦ 13k

Latest awards to Hervé Pagès

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 8 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 8 months ago, created an answer that has been accepted. For A: Extracting Coordinates of startcodon from Grangeslist
Scholar 9 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 9 months ago, created an answer that has been accepted. For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar 9 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 9 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 9 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Supporter 9 months ago, voted at least 25 times.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 10 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Error in GRanges: could not find symbol "recursive" in environment of the generi
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 12 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 12 months ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: XStringSet operations discard names - how to address?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Scholar 22 months ago, created an answer that has been accepted. For A: XStringSet operations discard names - how to address?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: pairwiseAlignments coordinate mapping?
Scholar 22 months ago, created an answer that has been accepted. For A: pairwiseAlignments coordinate mapping?
Scholar 22 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar 22 months ago, created an answer that has been accepted. For A: how much positions overlapped for each pair of the pairs obtained by findover
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromUCSC fails to download refLink table
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 149 users visited in the last hour