User: Tim Smith

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Tim Smith1.1k
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Posts by Tim Smith

<prev • 102 results • page 3 of 11 • next >
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Comment: C: Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt
... Try: chrom <- c(1:22,'X','Y') ________________________________ From: Karthik K N Cc: "bioconductor@r-project.org" Sent: Monday, July 23, 2012 7:46 AM Subject: Re: [BioC] Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt �Hello Tim, Thanks for the reply. I think t ...
written 7.3 years ago by Tim Smith1.1k
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Answer: A: Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt
... Seems to work with: chrom <- '1' xx <- getBM(attributes=c("hgnc_symbol", "3utr"),filters="chromosome_name",         values = chrom, mart = ensembl) ________________________________ From: Karthik K N To: bioconductor@r-project.org Sent: Monday, July 23, 2012 5:02 AM Subject: [BioC] Proble ...
written 7.3 years ago by Tim Smith1.1k
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Package Gviz: boxplot question
... Hi, I was using Gviz package to create a boxplot. I understand that Gviz uses "panel.bwplot" to create the boxplot. Is there any way that I can remove the dashed line surrounding each pair of boxplots? Here is some sample code: ############# library(Gviz) thisdata <- matrix(sample(1:100,60) ...
gviz written 7.3 years ago by Tim Smith1.1k
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Comment: C: GSEA with methylation data
... Hi Wen, Thanks for the reply! Do you know a bioconductor package that will do what the Broad GSEA tool does? thanks! ________________________________ From: wenhuo hu Cc: bioc Sent: Sunday, May 20, 2012 12:01 PM Subject: Re: [BioC] GSEA with methylation data Hi Would you check this? http ...
written 7.4 years ago by Tim Smith1.1k
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GSEA with methylation data
... Hi, I wanted to conduct GSEA analysis on methylation data (illumina 27k). After conducting a differential analysis, I have a list of genes along with their pvalues and t-statistics. Is there a way that I can conduct a GSEA analysis with this data? Which packages should I be looking at? I have loo ...
written 7.4 years ago by Tim Smith1.1k • updated 7.4 years ago by Sean Davis21k
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SVA package: remove batch effects using ComBat
... Hi, I was exploring batch effects in my data. At this stage, I don't want to introduce the 'variable of interest' (i.e. 'cancer' in the vignette/example given in sva.pdf that is used to get 'mod' - the model matrix). Should I use the mod0 matrix (i.e. the NULL matrix) as an input to the ComBat func ...
sva written 7.5 years ago by Tim Smith1.1k
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Biostrings: PWM with background probabilities
... Hi, I wanted to make a pwm with a frequency table. However, the background frequencies are given by a separate table. How can I incorporate these into the pwm? For example, my frequency table is:   1  2 3 4 5 6 7 8  9 10 A 3  3 1 2 1 5 4 2  3  6 G 2  1 2 5 4 3 3 3  1  5 C 8 10 7 6 7 6 7 8 10  0 T ...
go written 7.9 years ago by Tim Smith1.1k
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seqLogo package: sequence logo graph with background frequency?
... Hi, I had a question about the package/function seqLogo. I had a set of sequences for which I want to plot the sequence Logo. However, the background frequencies are not 1/4. I have another matrix with the background frequencies. How can I incorporate these in the seqLogo too? For example, my sequ ...
seqlogo written 7.9 years ago by Tim Smith1.1k
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biomaRt query ??
... Hi, I wanted to determine the locations for all the alternative splicing sites. I've made the query in biomaRt, but am not sure if this is giving me what I want. Any help would be appreciated! ##### library(biomaRt) ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") atb2 <- c("dbas ...
biomart written 8.0 years ago by Tim Smith1.1k • updated 8.0 years ago by Rhoda Kinsella660
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rtracklayer error?
... Hi, I was just trying out the rtracklayer package with the example given in the bioinformatics paper on rtracklayer. Here is my code and the error statement: > library(IRanges) > library(rtracklayer) > data(targets) > tt <- >with(targets,GenomicData(IRanges(start,end),target,stra ...
rtracklayer written 8.4 years ago by Tim Smith1.1k • updated 8.4 years ago by Michael Lawrence11k

Latest awards to Tim Smith

Centurion 5.4 years ago, created 100 posts.
Popular Question 5.4 years ago, created a question with more than 1,000 views. For biomaRt: retrieve exon sequence, start and end positions
Popular Question 5.4 years ago, created a question with more than 1,000 views. For org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Mapping gene symbols to gene names (org.Hs.eg.db?)
Popular Question 5.4 years ago, created a question with more than 1,000 views. For org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
Popular Question 5.4 years ago, created a question with more than 1,000 views. For installing 'lme4' package fails
Popular Question 5.4 years ago, created a question with more than 1,000 views. For GSEA with methylation data
Popular Question 5.4 years ago, created a question with more than 1,000 views. For org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
Popular Question 5.4 years ago, created a question with more than 1,000 views. For biomaRt: refseq gene details
Popular Question 5.4 years ago, created a question with more than 1,000 views. For biomaRt query: retrieve exon locations etc
Popular Question 5.4 years ago, created a question with more than 1,000 views. For UCSC: convert from hg18 to hg19 - rtracklayer?
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Visualizing KEGG pathways
Popular Question 5.4 years ago, created a question with more than 1,000 views. For installing 'lme4' package fails
Popular Question 5.4 years ago, created a question with more than 1,000 views. For SNP to Gene mapping (GWAS)
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Package/Function to calculate CpG density
Popular Question 5.4 years ago, created a question with more than 1,000 views. For GOstats: Listing genes from hyperGTest
Great Question 5.4 years ago, created a question with more than 5,000 views. For Mapping gene symbols to gene names (org.Hs.eg.db?)
Popular Question 5.4 years ago, created a question with more than 1,000 views. For GOstats: Listing genes from hyperGTest

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