User: RT

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RT330
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Posts by RT

<prev • 139 results • page 1 of 14 • next >
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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 6 weeks 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 6 weeks 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 9 weeks 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 14 months ago by RT330 • updated 4 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 15 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 15 months ago by RT330 • updated 15 months ago by Santosh Anand3.5k
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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 16 months ago by RT330 • updated 15 months ago by Santosh Anand3.5k
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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 16 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 17 months ago by RT330 • updated 17 months ago by EagleEye5.5k
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Comment: C: Macs2 failed for pooled samples
... I am very confused now. I actually started following IDR pipeline. Does not it recommend to run macs2 on both individual replicates and pooled replicates? https://sites.google.com/site/anshulkundaje/projects/idr ...
written 17 months ago by RT330

Latest awards to RT

Popular Question 22 days ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 7 weeks 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 6 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Great Question 6 months ago, created a question with more than 5,000 views. For How to extract all the mapped reads from bwa output
Great Question 6 months ago, created a question with more than 5,000 views. For How To Correctly Classify Gene Families?
Popular Question 6 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Great Question 11 months ago, created a question with more than 5,000 views. For How To Correctly Classify Gene Families?
Popular Question 11 months ago, created a question with more than 1,000 views. For loss of function prediction
Popular Question 11 months ago, created a question with more than 1,000 views. For Mapping coordinates from gff file to individual gene
Popular Question 11 months ago, created a question with more than 1,000 views. For Using ML tree or bootstrapped tree
Popular Question 11 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Student 13 months ago, asked a question with at least 3 up-votes. For Limma Package For Differential Expression Between Control And Stress
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 14 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 15 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 17 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 18 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
Great Question 19 months ago, created a question with more than 5,000 views. For Limma Package For Differential Expression Between Control And Stress
Popular Question 20 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 23 months ago, created a question with more than 1,000 views. For Best Program For Recombination Detection In Msa
Popular Question 23 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree

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