User: jaime.alvarez.benayas

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New User
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Spain
Last seen:
1 year, 5 months ago
Joined:
4 years, 7 months ago
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j********************@gmail.com

Posts by jaime.alvarez.benayas

<prev • 8 results • page 1 of 1 • next >
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Answer: A: gplots heatmap.2 scale function not generating Z-scores between -1 to +1
... 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.benayas10
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Comment: C: gplots heatmap.2 scale function not generating Z-scores between -1 to +1
... 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.benayas10
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gplots heatmap.2 scale function not generating Z-scores between -1 to +1
... 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 ...
scale R heatmap.2 gplots written 19 months ago by jaime.alvarez.benayas10 • updated 4 months ago by samkioko270
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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.benayas10
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Bedtools coverage adding feature scores
... 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 ...
bedtools score coverage written 3.5 years ago by jaime.alvarez.benayas10 • updated 22 months ago by Alex Reynolds29k
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Answer: A: Saturation analysis on downstream processed reads, fitting formula in data
... 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.benayas10
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Comment: C: Saturation analysis on downstream processed reads, fitting formula in data
... Sorry, I redirected the question at Seqanswers ...
written 3.8 years ago by jaime.alvarez.benayas10
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Saturation analysis on downstream processed reads, fitting formula in data
... 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 ...

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

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