User: Sonali Arora

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Sonali Arora360
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Posts by Sonali Arora

<prev • 21 results • page 2 of 3 • next >
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Answer: A: Download the stats of Bioconductor
... Hi Lluis, Here are some statistics in our latest newsletter -  http://www.bioconductor.org/help/newsletters/2015_January/#project-statistics Also our dashboard has some stats -  http://www.bioconductor.org/dashboard/ Thanks, Sonali.  ...
written 2.8 years ago by Sonali Arora360
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Answer: A: how can I tell if a RNAseq BAM file is paired end or single end ?
... Hi Stephen, Rsamtools (devel version) has a new function testPairedEndBam which returns TRUE if the BAM file contains paired end reads, FALSE otherwise.  library(Rsamtools) fl <- system.file("extdata", "ex1.bam", package="Rsamtools") testPairedEndBam(fl) [1] TRUE packageVersion("Rsamtools") ...
written 2.9 years ago by Sonali Arora360 • updated 2.9 years ago by Dan Tenenbaum ♦♦ 8.2k
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Comment: C: Google hangout on Wed December 10th for new package authors
... Thanks for joining us today for the Webinar! For those who missed it today, a video recording is now available at : https://www.youtube.com/watch?v=QfqaK_BHebU   ...
written 2.9 years ago by Sonali Arora360
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News: Course Material from Latest Bioconductor Course (Oct 27 -29, 2014)
... Hi everyone,  Course Material  from the latest Biocondcutor course held in Seattle from Oct 27-29, 2014 is now available. We also recorded a few videos this time to give users a flavor of what to expect from a typical Bioconductor Course. A big thank you to all the people who joined us in Seattle ...
news course-material video written 3.0 years ago by Sonali Arora360
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Answer: A: keepStandardChromosomes doesn't respect ordering
... Hi Jim, We have just added those changes to release version of GenomeInfoDb. You can either use svn and get the latest code from release version branch now or use biocLite() and get it tomorrow.  Let us know if you have any questions Thanks, Sonali.  ...
written 3.1 years ago by Sonali Arora360
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Answer: A: keepStandardChromosomes doesn't respect ordering
... Hi Jim, which version of GenomeInfoDb are you using ? Please update it using biocLite("GenomeInfoDb") Your example works for me.  > library(GenomeInfoDb) > library(TxDb.Mmusculus.UCSC.mm10.knownGene) > gns <- genes(TxDb.Mmusculus.UCSC.mm10.knownGene) > gns2 <- keepStandardChr ...
written 3.1 years ago by Sonali Arora360 • updated 3.1 years ago by James W. MacDonald45k
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Answer: A: Problem in K- means clustering
... Hi Aditya, You have a typo error in your code . It should be - i <- c(2) instead of irm(list=ls()) >dat2<- mtcars >kmax<-c(100) ># If there are less than 100 genes or arrays ># make the max. no. of cluster equal to the ># number of genes or arrays >if(nrow(dat2)<100 ...
written 3.2 years ago by Sonali Arora360
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Announcing Bioconductor's youTube Channel
... Hi, We are pleased to announce Bioconductor's youTube Channel. https://www.youtube.com/user/bioconductor Please go check it out and let us know what topics you would like to see Videos on ! If you are a package developer, wondering how you can submit a Instructional video for your package? Sim ...
go written 3.3 years ago by Sonali Arora360
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Answer: A: GenomeinfoDB
... Hi Isran I have just added support for Mus musculus in version 1.1.10 of GenomeInfoDb > library(GenomeInfoDb) > names(genomeStyles()) [1] "Arabidopsis_thaliana" "Caenorhabditis_elegans" "Cyanidioschyzon_merolae" [4] "Drosophila_melanogaster" "Homo_sapiens" "Mus_musculus" [7] "Oryza_s ...
written 3.4 years ago by Sonali Arora360
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Answer: A: Renaming the seqlevels in a transcript database from GenomicFeatures
... Hi Fong, A TranscriptDb cannot be directly subset with 'keepSeqlevels' and 'dropSeqlevels'. But the GRanges or GRangesLists extracted from the TranscriptDb can be subset. Below I show an example for how to extract GRanges, subset and change the chromosome name style from "UCSC" to "NCBI" ( ie from ...
written 3.4 years ago by Sonali Arora360

Latest awards to Sonali Arora

Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Ensembl release 80 is out!
Scholar 19 months ago, created an answer that has been accepted. For A: Normal Patient Samples from GSE62944
Popular Question 19 months ago, created a question with more than 1,000 views. For Epigenomics RoadMap Project files now accessible via AnnotationHub
Popular Question 19 months ago, created a question with more than 1,000 views. For Course Material from BioC 2015: Where Software and Biology Connect
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Ensembl release 80 is out!
Appreciated 2.3 years ago, created a post with more than 5 votes. For Epigenomics RoadMap Project files now accessible via AnnotationHub
Appreciated 2.5 years ago, created a post with more than 5 votes. For Epigenomics RoadMap Project files now accessible via AnnotationHub
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Ensembl release 80 is out!

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