User: RT

gravatar for RT
RT330
Reputation:
330
Status:
Trusted
Location:
European Union
Last seen:
4 days, 6 hours ago
Joined:
7 years, 5 months ago
Email:
t***********@gmail.com

Posts by RT

<prev • 142 results • page 1 of 15 • next >
0
votes
0
answers
76
views
0
answers
Comment: C: expression evidence for overlapping genes
... correct me if I am asking a dumb question. How does stranded RNA-seq solves my problem. Overlapping gene can exist in different frame, not necessarily from different strand. ...
written 4 days ago by RT330
0
votes
0
answers
76
views
0
answers
expression evidence for overlapping genes
... Hi All, Can anyone point out to me method/tool to get the expression evidence for overlapping genes. Thanks, Rit ...
rna-seq written 4 days ago by RT330
0
votes
0
answers
404
views
0
answers
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 10 months ago by RT330
0
votes
0
answers
365
views
0
answers
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 12 months ago by RT330
0
votes
0
answers
365
views
0
answers
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 12 months ago by RT330
0
votes
0
answers
3.5k
views
0
answers
Comment: 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 13 months ago by RT330
0
votes
1
answer
726
views
1
answer
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 2.1 years ago by RT330 • updated 15 months ago by Biostar ♦♦ 20
0
votes
1
answer
2.3k
views
1
answers
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 2.1 years ago by RT330
4
votes
1
answer
2.3k
views
5 follow
1
answer
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 2.1 years ago by RT330 • updated 2.1 years ago by Santosh Anand4.8k
0
votes
1
answer
1.2k
views
1
answer
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 2.2 years ago by RT330 • updated 2.1 years ago by Santosh Anand4.8k

Latest awards to RT

Popular Question 3 months ago, created a question with more than 1,000 views. For Gene id to gene name mapping
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
Popular Question 4 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 8 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 9 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Great Question 9 months ago, created a question with more than 5,000 views. For How to extract all the mapped reads from bwa output
Popular Question 9 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 9 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 10 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 11 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Popular Question 12 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 Running Codeml On Unrooted Tree
Great Question 17 months ago, created a question with more than 5,000 views. For How To Correctly Classify Gene Families?
Great Question 17 months ago, created a question with more than 5,000 views. For How to extract all the mapped reads from bwa output
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 22 months ago, created a question with more than 1,000 views. For Using ML tree or bootstrapped tree
Popular Question 22 months ago, created a question with more than 1,000 views. For Mapping coordinates from gff file to individual gene
Popular Question 22 months ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree
Great Question 22 months ago, created a question with more than 5,000 views. For How To Correctly Classify Gene Families?
Popular Question 22 months ago, created a question with more than 1,000 views. For loss of function prediction
Student 2.0 years ago, asked a question with at least 3 up-votes. For Limma Package For Differential Expression Between Control And Stress
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Using ML tree or bootstrapped tree
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Running Codeml On Unrooted Tree

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1638 users visited in the last hour