User: nick

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nick90
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Posts by nick

<prev • 19 results • page 1 of 2 • next >
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Answer: A: How to deside gene CNVs from .cnr outputs
... To merge bins you need to run `cnvkit.py segment` to create `.cns` files. Assuming a diploid genome: - Log2(CR) = -1 → CR = 0.5 → 1 copy (of a segment/gene). - Log2(CR) = 0 → CR = 1 → copies - Log2(CR) = +1 → = 2 → 4 copies - Log2(CR) = 0.58 → = 1.5 → copies Of course you have to consider a bit o ...
written 11 weeks ago by nick90
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Comment: C: confused about how to run pipeline
... I think there's an error in the documentation because it shows that you have to pass an access file but first you need to run `cnvkit.py access` to create it. Do what Paul suggests in his answer. ...
written 11 weeks ago by nick90
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Comment: C: How To Compare Gene Expression And Methylation Level Of A Gene
... As suggested in Neilfws's comment I decided to choose the probe with the highest variance. ...
written 5 months ago by nick90
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Biopython pairwise2 alignment: is one_alignment the best alignment?
... I started using `pairwise2.align` function from [Biopyton][1] with the `one_alignment` set to True. I was wondering if that single alignment returned is the best one. With Smith-Waterman it should be but I'm not sure if that's what's been implemented. [1]: https://github.com/biopython/biopython/b ...
alignment biopython written 11 months ago by nick90 • updated 11 months ago by rayoub110
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Comment: C: TCGA & METABRIC Breast Cancer Subtype Survival Curve
... [here][1] or using R package TCGAbiolinks [1]: https://portal.gdc.cancer.gov/ ...
written 17 months ago by nick90
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Answer: A: TCGAquery function from TCGAbiolinks
... Have you tried with`GDCquery`? ...
written 19 months ago by nick90
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Comment: C: DNA methylation analysis with RnBeads: start analysis from Beta-values
... Yes, sorry I didn't specify that. ...
written 2.7 years ago by nick90
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DNA methylation analysis with RnBeads: start analysis from Beta-values
... I am trying to use RnBeads to analyze DNA-methylation data, but I already have a matrix of beta-values. I cannot find a way to import data in that format and launch a differential analysis. Has anyone encountered the same problem? ...
dna-methylation rnbeads written 2.7 years ago by nick90 • updated 2.7 years ago by andrew.j.skelton735.5k
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Visually display genomic location of a list of genes
... I have a list of human genes (order matters, since they have been clustered together) and I'd like to see their position in the genome. I was thinking about something like this: two axes one above the other; first axis represent the genome displayed as one chromosome after the other; second axis ...
genome R written 3.6 years ago by nick90 • updated 3.6 years ago by Jautis270
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Comment: C: abyss-fac: command not found on Kubuntu 14.04
... It worked! I didn't know this difference, thank you. ...
written 4.1 years ago by nick90

Latest awards to nick

Popular Question 13 days ago, created a question with more than 1,000 views. For DNA methylation analysis with RnBeads: start analysis from Beta-values
Appreciated 5 months ago, created a post with more than 5 votes. For How To Compare Gene Expression And Methylation Level Of A Gene
Popular Question 11 months ago, created a question with more than 1,000 views. For DNA methylation analysis with RnBeads: start analysis from Beta-values
Popular Question 17 months ago, created a question with more than 1,000 views. For abyss-fac: command not found on Kubuntu 14.04
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Tcga Data From Synapse: Whitelisting Criteria
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How To Compare Gene Expression And Methylation Level Of A Gene
Student 4.9 years ago, asked a question with at least 3 up-votes. For How To Compare Gene Expression And Methylation Level Of A Gene

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