User: goldberg.jm

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goldberg.jm10
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Posts by goldberg.jm

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Use biomaRt to get pre-calculated transcription factor binding sites (TFBS) for
... Thanks James. Before I try liftOver, I'll see if I can use TFBStools (https://bioconductor.org/packages/release/bioc/html/TFBSTools.html) to calculate the sites by applying PSSMs to the sequence. Best, Jon ...
written 4 days ago by goldberg.jm10
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Comment: C: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
... I ended up doing an ugly cludge... I read in the small, selected vcf as a data.frame and mapped its rs numbers to the names of the small GRranges object via genome start coordinate of the variant. I realize that this could lead to errors if more than one rs number has the same start. When I get a ch ...
written 5 days ago by goldberg.jm10
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Comment: C: Use biomaRt to get pre-calculated transcription factor binding sites (TFBS) for
... I do know how to use biomaRt to access archived versions of "Ensembl Genes..." (see code below), just not for "Ensembl Regulation..." useMart(host='grch37.ensembl.org',biomart='ENSEMBL_MART_ENSEMBL',dataset='hsapiens_gene_ensembl') # ...
written 5 days ago by goldberg.jm10
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Use biomaRt to get pre-calculated transcription factor binding sites (TFBS) for GRCh37
... Hi All, I wish to use Bioconductor/biomaRt to get pre-calculated transcription factor binding site (TFBS) results for GRCh37. To do this (for GRCh38) at the ensembl biomart interface (http://www.ensembl.org/biomart/martview/), under "-CHOOSE DATABASE-" I select "ENSEMBL REGULATION 92", and under " ...
biomart written 5 days ago by goldberg.jm10 • updated 4 days ago by James W. MacDonald46k
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Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
... Hi All, Could you please let me know how to get rsnumbers using using IntronVariants()? intron_regions <- IntronVariants() head(locateVariants(vcf_mod, enstxdb, intron_regions)) 'select()' returned many:1 mapping between keys and columns GRanges object with 6 ranges and 9 metadata columns ...
variantannotation written 22 days ago by goldberg.jm10 • updated 16 days ago by Valerie Obenchain ♦♦ 6.5k
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Comment: C: RNA-seq read alignment best practices for low-input samples
... Yeah, you're right! Thanks for the suggestions on where to ask this. ...
written 7 months ago by goldberg.jm10
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RNA-seq read alignment best practices for low-input samples
... RNA-seq read alignment best practices for low-input samples Hi All, There are many ways to align RNA-seq reads to transcripts and genomes, and I am confused about which is best for my experiment. My goal is to do differential expression analysis on Plasmodium vivax data. The input is fastq files ...
alignment limma differential gene expression rsem rnaseq analysis written 7 months ago by goldberg.jm10 • updated 7 months ago by Aaron Lun20k
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Comment: C: Map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript ID or Refs
... In theory TXID/TXNAM - ENST mappings should be 1-to-1, right? Do you know why they are not? ...
written 19 months ago by goldberg.jm10
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Comment: C: Map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript ID or Refs
... Thank you... works like a charm! I really do want TXID-ENST pairings but it's good to see other examples as well. ...
written 19 months ago by goldberg.jm10
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Map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript ID or Refseq ID
... Hi All, How do I map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript IDs or Refseq IDs?  I know this must be a basic task, but I have been playing around with it and googling all afternoon and have not cracked it. I am sure Valerie Obenchain and many others can answer this easily. ...
annotationdbi written 19 months ago by goldberg.jm10 • updated 19 months ago by James W. MacDonald46k

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