User: Duke

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Duke210
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7 years, 7 months ago
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Posts by Duke

<prev • 21 results • page 1 of 3 • next >
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Comment: C: fastest way to get a gene list having certain GO term
... On 3/6/12 5:24 PM, Duke wrote: > On 3/6/12 3:47 PM, Duke wrote: >> Hi folks, >> >> I need some statistics for a certain GO term (for example, "DNA >> binding"), and I wonder what is the fastest way to archive the latest >> list of genes having that specific GO term. ...
written 7.6 years ago by Duke210
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Answer: A: fastest way to get a gene list having certain GO term
... On 3/6/12 3:47 PM, Duke wrote: > Hi folks, > > I need some statistics for a certain GO term (for example, "DNA > binding"), and I wonder what is the fastest way to archive the latest > list of genes having that specific GO term. There are now a number of > GO packages and I would l ...
written 7.6 years ago by Duke210
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fastest way to get a gene list having certain GO term
... Hi folks, I need some statistics for a certain GO term (for example, "DNA binding"), and I wonder what is the fastest way to archive the latest list of genes having that specific GO term. There are now a number of GO packages and I would like to hear/learn your experience regarding various differen ...
go written 7.6 years ago by Duke210
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Comment: C: DEXSeq without replicates?
... On 12/22/11 4:18 PM, Simon Anders wrote: > Hi > > On 2011-12-22 21:41, Duke wrote: >> I am testing the DEXSeq package with a public RNA-Seq data. >> Unfortunately this data set does not have replicates, only two set of >> data with two conditions. I tried DEXSeq but got er ...
written 7.8 years ago by Duke210
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DEXSeq without replicates?
... Hi folks, I am testing the DEXSeq package with a public RNA-Seq data. Unfortunately this data set does not have replicates, only two set of data with two conditions. I tried DEXSeq but got error. I checked the estimateDispersion function but there is no similar option like in DESeq where we can use ...
dexseq written 7.8 years ago by Duke210 • updated 7.8 years ago by Simon Anders3.6k
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Comment: C: biomaRt ensembl mmusculus does not contain all ensembl IDs (lincRNA, miRNA etc)?
... Hi Steffen, Thanks so much for quick response. Yes, removing entrezgene does help! Bests, D. On 4/18/11 4:41 PM, Steffen Durinck wrote: > Hi Duke, > > It looks like this is a BioMart server issue where the wrong type of > table join is made with the entezgene table. > If you remov ...
written 8.5 years ago by Duke210
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biomaRt ensembl mmusculus does not contain all ensembl IDs (lincRNA, miRNA etc)?
... Hi folks, Following instruction of biomaRt usage, I am trying to get information for our mmu data. The code I used was below: ---------- library(biomaRt) mart<- useDataset("mmusculus_gene_ensembl", useMart("ensembl")) ensTransIDs <- c("ENSMUST00000000001", "ENSMUST00000083463","ENSMUST000000 ...
mirna biomart written 8.5 years ago by Duke210 • updated 8.5 years ago by Steffen Durinck540
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GO with R and Bioconductor
... On 2/28/11 2:31 PM, Vincent Carey wrote: > On Mon, Feb 28, 2011 at 2:07 PM, Duke wrote: >> On 2/26/11 8:09 PM, Vincent Carey wrote: >>> On Sat, Feb 26, 2011 at 6:40 PM, Duke wrote: >>>> Hi Vincent, >>>> >>>> On 2/26/11 2:38 PM, Vincent Carey wro ...
transcription annotation go gostats biomart topgo gseabase goseq written 8.7 years ago by Duke210
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Comment: C: GO with R and Bioconductor
... On 2/26/11 8:09 PM, Vincent Carey wrote: > On Sat, Feb 26, 2011 at 6:40 PM, Duke wrote: >> Hi Vincent, >> >> On 2/26/11 2:38 PM, Vincent Carey wrote: >>> On Sat, Feb 26, 2011 at 12:00 PM, wrote: >>>> Dear colleagues, >>>> >>>> I ...
written 8.7 years ago by Duke210
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Comment: C: GO with R and Bioconductor
... Hi Vincent, On 2/26/11 2:38 PM, Vincent Carey wrote: > On Sat, Feb 26, 2011 at 12:00 PM, wrote: >> Dear colleagues, >> >> I used to download GO database from geneoncology.org and did some c++ coding to manipulate the data as I wished. Now I want to try my luck with R - Bioco ...
written 8.7 years ago by Duke210

Latest awards to Duke

Popular Question 7.6 years ago, created a question with more than 1,000 views. For GO with R and Bioconductor
Popular Question 7.6 years ago, created a question with more than 1,000 views. For DEXSeq without replicates?
Popular Question 7.6 years ago, created a question with more than 1,000 views. For find overlap of bed files of different length
Popular Question 7.6 years ago, created a question with more than 1,000 views. For DEXSeq without replicates?

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