User: RT

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RT330
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330
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European Union
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27 minutes ago
Joined:
6 years, 8 months ago
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Posts by RT

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Comment: C: 2x - University Research Fellows - Bioinformatics, University of Adelaide, Adela
... Hi David, The link given isn't working. Are these positions filled? Thanks, RT ...
written 6 weeks ago by RT330
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Comment: C: calculating dn/ds from codeml output
... Hi Biojl, thanks for the response. No, I have used a software from a collaborator and now I have to do he dn/ds calculations by hand as part of paper resubmission response. What I understand is fetching W2 values from ModelA where the likelihood score is maximum for different omega starting values ( ...
written 3 months ago by RT330
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calculating dn/ds from codeml output
... Hi everyone, I ran branch-site models and made the comparisons of likelihood values modelA vs modelA null and modelA vs m1a. The omega values used are 0,1,2 and 10. I now need to extract dn/ds of my gene. Can someone help me how to extract this from codeml output. Thanks, RT ...
codeml written 3 months ago by RT330
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Answer: A: Open positions at the Center for Molecular Oncology, MSKCC, New York
... Hi Cyriac, Since this post is modified two days ago, I am wondering if these positions are still open? Thanks, Reetu ...
written 4 months ago by RT330
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Data mining for 300 genes from GEO
... Hi All, I have a gene list of ~ 300 genes. I want to get from GEO all the high-throughput expression studies for these genes. I can write a R script to make this search with GEOsearch package. But I guess the package only allows for geneid/name based search. I was wondering if there is a way to sea ...
geo written 16 months ago by RT330 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: Select top differentially expressed genes based on both p-value and fold-change
... so what is the best way to select top genes? As I said, I was suggested to consider both p-values and fold-change and use rankproduct for this. Rankproduct is used for identification of DEGs. I am not sure how to apply it to foldchange and pvalue. Any other ideas of combining pval and fc for seelc ...
written 17 months ago by RT330
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Select top differentially expressed genes based on both p-value and fold-change
... I always selected top differentially expressed genes based on p-values (DESeq2 for differential-expr analysis). Just recently, someone suggested me to use both p-value and fold change to select top genes. I am little confused as p-values already take fold-change into consideration. Can someone shed ...
differential-expression deseq2 rna-seq written 17 months ago by RT330 • updated 17 months ago by Santosh Anand3.9k
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meme-suite: How does FIMO works?
... Dear All, I am new to motif identification area. From a set of sequences (~200), I want to search for a known motif and filter out sequences where the motif does not exist. My motif is 8bp long. A simple python search gave me too many random hits. Someone quickly suggested to me to use meme-tools a ...
meme-suite motif identification fimo written 18 months ago by RT330 • updated 17 months ago by Santosh Anand3.9k
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pybedtools change fasta headers
... I am using pybedtools to get promoter sequences for my genes of interest. I am almost done with the script. But I would also like to include gene names in the fasta headers. By default, it only include corrdinates in fasta headers. Below is my script: >coords=Chr1 1000 2000 forward 1 + >a ...
python pybedtools written 18 months ago by RT330
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Chip-seq on pooled replicates
... Dear All, Can someone please help me to understand why for ChIP-seq we should not merge the biological replicates before peak calling. I read in several papers, peaks calling is done on individual replicates. I am struggling to understand this. Ideally if I merge replicates I should have more power ...
chip-seq pooled replicates written 19 months ago by RT330 • updated 19 months ago by EagleEye5.7k

Latest awards to RT

Popular Question 4 days ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Great Question 8 days ago, created a question with more than 5,000 views. For How to extract all the mapped reads from bwa output
Popular Question 23 days ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 25 days ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 3 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 4 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Great Question 8 months ago, created a question with more than 5,000 views. For How to extract all the mapped reads from bwa output
Popular Question 8 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Great Question 8 months ago, created a question with more than 5,000 views. For How To Correctly Classify Gene Families?
Popular Question 8 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 13 months ago, created a question with more than 1,000 views. For Using ML tree or bootstrapped tree
Popular Question 13 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 13 months ago, created a question with more than 1,000 views. For Mapping coordinates from gff file to individual gene
Great Question 13 months ago, created a question with more than 5,000 views. For How To Correctly Classify Gene Families?
Popular Question 13 months ago, created a question with more than 1,000 views. For loss of function prediction
Popular Question 15 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Student 15 months ago, asked a question with at least 3 up-votes. For Limma Package For Differential Expression Between Control And Stress
Popular Question 15 months ago, created a question with more than 1,000 views. For Using ML tree or bootstrapped tree
Popular Question 16 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 17 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 19 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 19 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 20 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree

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