User: jaime.alvarez.benayas
- Reputation:
- 10
- Status:
- New User
- Location:
- Spain
- Last seen:
- 1 year, 5 months ago
- Joined:
- 4 years, 7 months ago
- Email:
- j********************@gmail.com
Posts by jaime.alvarez.benayas
<prev
• 8 results •
page 1 of 1 •
next >
1
vote
1
answer
2.7k
views
1
answers
... Sorry, silly mistake, as you say, I wasn't understanding Z-scores correctly.
So there are two issues here: one is that the Z-scores can go beyond -1 and +1 so there isn't a problem. The other one is that I made a mistake in my code since the "scale" function scales by columns and not rows, therefor ...
written 19 months ago by
jaime.alvarez.benayas • 10
1
vote
1
answer
2.7k
views
1
answers
... Sorry, silly mistake, as you say, I wasn't understanding Z-scores correctly.
So there are two issues here: one is that the Z-scores can go beyond -1 and +1 so there isn't a problem.
The other one is that I made a mistake in my code since the "scale" function scales by columns and not rows, therefor ...
written 19 months ago by
jaime.alvarez.benayas • 10
3
votes
1
answer
2.7k
views
1
answer
... Hello,
I am trying to display a heatmap using gplots heatmap.2 function, borrowing the data from:
http://www.opiniomics.org/you-probably-dont-understand-heatmaps/
My problem is with regards to the scale="row" parameter. In theory, this is getting the raw data and performing a scaling (subtracting ...
written 19 months ago by
jaime.alvarez.benayas • 10
• updated
4 months ago by
samkioko27 • 0
0
votes
3
answers
19k
views
3
answers
Comment:
C: ATAC-seq peak calling with MACS
... I was wondering which parameters to use too. Assuming this is the pipeline ENCODE is using (https://github.com/kundajelab/atac_dnase_pipelines), specifically the ATAC-seq pipeline protocol definition (https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit?usp=sharing)
...
written 2.8 years ago by
jaime.alvarez.benayas • 10
0
votes
2
answers
1.8k
views
2
answers
... I am trying to calculate the coverage of features in a gff file and a bed file containing the windows.
The bed file (windows_test.bed), note 0 based:
chr1 0 50 1
chr1 50 100000 2
The gff file (test.gff), note 1 based:
chr1 Program HS4 51 1003535 ...
written 3.5 years ago by
jaime.alvarez.benayas • 10
• updated
22 months ago by
Alex Reynolds ♦ 29k
0
votes
2
answers
1.6k
views
2
answers
... Thanks for the hint John, checked and it got me in the right tracks to fix the problem:
>>> type(params["V"].value)
>>> type(params["K"].value)
>>> type(x)
Apparently I was using simple arrays as inputs and when operating def obj(params, x, y) ...
written 3.8 years ago by
jaime.alvarez.benayas • 10
0
votes
2
answers
1.6k
views
2
answers
... Sorry, I redirected the question at Seqanswers ...
written 3.8 years ago by
jaime.alvarez.benayas • 10
2
votes
2
answers
1.6k
views
2
answers
... Hello,
I have DNA sequencing data enriched for a region of DNA, after mapping and doing further processing downstream analysis (including de-duplication of reads) I end up with a subset of informative reads.
I have performed sampling (from 10% of the input sequenced reads to 100%), after each samp ...
written 3.8 years ago by
jaime.alvarez.benayas • 10
Latest awards to jaime.alvarez.benayas
Scholar
19 months ago,
created an answer that has been accepted.
For A: gplots heatmap.2 scale function not generating Z-scores between -1 to +1
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For Saturation analysis on downstream processed reads, fitting formula in data
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1293 users visited in the last hour