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• ChipPeakAnno:getAnnotation using UCSC instead of ensembl
  Hello, For various reasons, I am obligated to analyze RNA and Chip sequencing data with a UCSC r...
• Adding gene names to differential gene expression results in DESeq2
  The codes and instructions for annotating gene names to the result table for differential gene ex...
• ensembl annotation coordinate did not match that from UCSC genome browser using ucscTableQuery
  Hi, all I don't know if it is just by chance, I was retrieving sequence for ENSMUST00000027587usi...
• BSgenomes vs ENSEMBL
  Dear list, I am a novice in genome builds and have therefore some basic questions. My ultimate ...
• Ensembl mouse proteins
  Hi, I have tried to download the mouse protein sequences from Biomart Ensembl. I only received 2...
• GenomicFeatures coordinates UCSC
  Hi, I would like to know if the annotation coordinates extracted with GenomicFeatures from UCSC a...
• Gviz - Cannot plot exons from gencode GTF files
  Hello, I am trying to use GViz for plotting genes annotations from GTF/GFF files.  It works nic...
• is database RefSeq achievable from any Bioconductor package
  Hi, On Mon, May 31, 2010 at 8:40 AM, wrote: > The Biologist we work with has brought my att...
• some problems of easyRNASeq� : about the gtf files
  I want to use easyRNASeq to get exon counts. But I found a strange thing: I have two human anno...
• ENCODE integrated genomic annotation data access
  I try to use ENCODE annotation data in my own data analysis. I couldn’t find a introductory tutor...
• Problem with mapp ensemble protein ids to entrez ids using org.Hs.eg.db
  I am using org.Hs.eg.db to map ensemble ids (from Stringdb) to entrez ids. I used to be able to m...
• Is there a place to download GenomicFeatures' sqlite from ensembl.
  Dear all, I am trying to make TranscriptDb Object. First I used makeTranscriptDbFromUCSC, it is n...
• easyRNASeq Error in counting from C.elegans
  Dear All and Nico, Have anyone be able to do the counting from C.elegans? Here is what I tried...
• Working with ensembl 73 & BSGenome
  Hi, I'm working with the latest annotation set from Ensembl (ens73) which is based on the patche...
• IRanges, GenomicRanges, GenomicFeatures?
  Hello list members, For a RNA-seq analysis, what would you suggest to use to convert raw- sequen...
• Conservation tracks in BioC?
  Would like to get some advice on the best way to access Conservation data from UCSC like the hum...