User: Davy

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Davy210
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6 years, 8 months ago
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6 years, 9 months ago
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Posts by Davy

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16
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Transcription Factor Binding Sites
... Hi All, I'm trying to find the TFBS poisition weight matrices for the TFs snail, slug, twist, and smad 4 in humans None of these are in JASPAR, and I've had no luck with TRANSFAC either. Anyone have any idea where I might be able to get these matrices. Failing the matrices I could calculate them my ...
binding R transcription pssm written 6.7 years ago by Davy210 • updated 2.4 years ago by Biostar ♦♦ 20
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Comment: C: What To Do With Enriched Tfbss
... Great answer!!! In regards to your second suggestion. Have any pointers on how one might go about this? A paper perhaps where this was done. Thanks again! ...
written 6.7 years ago by Davy210
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Comment: C: Optimal Scripting Language Config For Bioinfomatics In Windows 7
... Eclipse does indeed have plugins for Perl. They pretty good, but I would not AS good as PyDev. That might just be because I prefer python though. Eclipse also has a plugin for R (statEt) although I use Rstudio and the Revolution R. ...
written 6.7 years ago by Davy210
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What To Do With Enriched Tfbss
... Hi All, I performed a transcription factor binding site enrichment analysis in R. Briefly, I have a co-regulated pathway in a disease state, and I wanted to see if there were any TFs that were significantly enriched within the promoter sequences of the genes in this pathway. So I took 5000 bp upstre ...
binding enrichment promoter transcription written 6.7 years ago by Davy210 • updated 6.7 years ago by Larry_Parnell16k
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Comment: C: How To Retrieve Gene Family Alignment Data From Ensembl Database
... Your question is very ambiguous. Please try to more specific so that we can help. ...
written 6.7 years ago by Davy210
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Answer: A: How To Retrieve Upstream Sequences Of A Single Gene From Multiple Bacterial Spec
... IF you are familiar with Perl the eutils should be able to sort you out. http://www.ncbi.nlm.nih.gov/books/NBK25501/ ...
written 6.7 years ago by Davy210
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Comment: C: Going For The Right P-Value With Limma
... Where is the up-vote one million button? Excellent post. I would add, that if Tomas can provide more details about his experiment we might be better able to advise on what to do next. What it a simple treatment versus control. Does one group have a particular trait you are interested in looking at? ...
written 6.8 years ago by Davy210
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Comment: C: Recommend Some Software/Package For Go Enrichment & Visualization
... Are you familiar with R and Bioconductor/BiomaRt?? What species are you working on? ...
written 6.8 years ago by Davy210
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Answer: A: Subsetting Affybatch
... Perhaps someone might correct me but I think that if you know the probe ids of the probes you want to remove then you can do: probes.to.remove <- c(<probe ids go here>) affy.batch.data <- affy.batch.data[!(featurenames(affy.batch.data) %in% probes.to.remove), ] ...
written 6.8 years ago by Davy210
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Comment: C: Dna Sequencers Output Read Length - Now
... @Mikael, do you know how recent this is? Would be very useful if within the last year or so. Cheers! ...
written 6.8 years ago by Davy210

Latest awards to Davy

Student 6.7 years ago, asked a question with at least 3 up-votes. For Transcription Factor Binding Sites
Student 6.7 years ago, asked a question with at least 3 up-votes. For What To Do With Enriched Tfbss
Appreciated 6.8 years ago, created a post with more than 5 votes. For A: Convert Plink Ped Format Into Hapmap Format?
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: Convert Plink Ped Format Into Hapmap Format?

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