User: Eisuan

gravatar for Eisuan
Eisuan0
Reputation:
0
Status:
New User
Last seen:
1 month, 1 week ago
Joined:
1 year, 6 months ago
Email:
d*************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by Eisuan

<prev • 13 results • page 1 of 2 • next >
0
votes
0
answers
106
views
0
answers
Managing duplicates in hierarchical clustering analysis of time-course RNA-seq data
... Hello everyone, I have questions regarding how to design properly hierarchical clustering of time-course RNA-seq data. The data consist of seven time points and two replicates for each time point. I already performed data QC, DESeq2 counts normalization and DE analysis (based upon LRT). I utilize R ...
R rna-seq written 7 weeks ago by Eisuan0
0
votes
0
answers
127
views
0
answers
Comment: C: Advice on how to retrieve and analyze a set of promoters of many genes / to find
... Hello! I am working on human lines. Are there some examples that I could use as a reference? ...
written 11 weeks ago by Eisuan0
0
votes
0
answers
127
views
0
answers
Advice on how to retrieve and analyze a set of promoters of many genes / to find putative TFs involved in gene expression reguolation based upon a list of co-expressed genes
... Hello! I would ask you some questions. Basically I have a list of genes that are co-expressed during a process of differentiation. This is based upon time-course RNA-seq data of which I have performed hierarchical clustering on a set of genes related to different GO terms. Basically, I pasted th ...
genome R human written 11 weeks ago by Eisuan0
0
votes
0
answers
100
views
0
answers
UCSC table broswer track for obtaining BED with ENSMUSG identifiers / E
... Hello everyone! I need to get a mouse genome reference for applying bedtools intersect to a set of ChIP-seq peaks. On the UCSC table browser, which tracks allow to get ENSMUSG identifiers? I was able to retrieve ENSMUST only. ...
genome written 3 months ago by Eisuan0
0
votes
0
answers
272
views
0
answers
Comment: C: Conversion RPKM in counts using R
... Thank you for your reply. Yes, I could ask directly for the counts matrix. However, I was wondering if it could possible to retrieve the information in another way. ...
written 7 months ago by Eisuan0
0
votes
0
answers
272
views
0
answers
Conversion RPKM in counts using R
... Hello everyone! Is there any R function able to convert RPKM in counts? I would like to follow the workflow analysis of a DESeq2 tutorial. Unfortunately, I have two xlsx files of this RNA-seq analysis: one containing avg counts and the other one containing RPKM for each replicate. What I would lik ...
R rna-seq written 7 months ago by Eisuan0
3
votes
1
answer
263
views
1
answer
Evaluating evolutionary conservation of TF binding site predictions
... Hello everyone! I am trying to validate TF binding site predictions through evolutionary conservation evaluation. Since this moment I was lucky since the potential TF binding sites are encompassed in a few of the very conserved regions of this promoter (human vs mouse). However, I have never taken ...
genome promoter written 10 months ago by Eisuan0 • updated 10 months ago by Kevin Blighe63k
0
votes
1
answer
303
views
1
answers
Comment: C: Tool for obtaning genes modulated by a list of TF
... Thank you so much :) Your suggestions were really helpfull ...
written 11 months ago by Eisuan0
2
votes
1
answer
303
views
1
answer
Tool for obtaning genes modulated by a list of TF
... Given a list of TFs, are there tools that are able to give me the list of genes known to be regulated by these TFs? ...
gene written 11 months ago by Eisuan0 • updated 11 months ago by natasha.sernova3.7k
0
votes
0
answers
632
views
0
answers
Comment: C: Trascription factor binding sites prediction using FIMO
... It is funny because all the time I try to apply some tools that search matches in a database using this promoter region I find few / no results. I had the same experience using AME (Meme Suite) for this region. I am pretty sure there are no problems with the promoter sequence I am using. ...
written 11 months ago by Eisuan0

Latest awards to Eisuan

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1679 users visited in the last hour