User: nick

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nick80
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Posts by nick

<prev • 17 results • page 1 of 2 • next >
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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 9 weeks ago by nick80
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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 8 months ago by nick80 • updated 8 months ago by rayoub100
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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 14 months ago by nick80
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Answer: A: TCGAquery function from TCGAbiolinks
... Have you tried with`GDCquery`? ...
written 16 months ago by nick80
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Comment: C: DNA methylation analysis with RnBeads: start analysis from Beta-values
... Yes, sorry I didn't specify that. ...
written 2.4 years ago by nick80
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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 2.4 years ago by nick80 • updated 2.4 years ago by andrew.j.skelton735.4k
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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 3.3 years ago by nick80 • updated 3.3 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 3.8 years ago by nick80
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abyss-fac: command not found on Kubuntu 14.04
... I installed ABySS following the instructions from the official documentation. >sudo apt-get install abyss and then proceeded with a simple test >wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz >tar xzvf test-data.tar.gz >abyss-pe k=25 name=te ...
next-gen abyss sequencing written 3.8 years ago by nick80
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Glioblastoma CpG Methylator Phenotype: where can I find sample barcodes/names?
... Hi, I need to retrieve the list of TCGA glioblastoma samples that were classified as G-CIMP (Noushmehr et al., 2010). In the paper they are not listed (or I wasn't able to find any information about them). Does anybody know where to fin them? ...
glioblastoma tcga written 4.0 years ago by nick80

Latest awards to nick

Appreciated 8 weeks ago, created a post with more than 5 votes. For How To Compare Gene Expression And Methylation Level Of A Gene
Popular Question 8 months ago, created a question with more than 1,000 views. For DNA methylation analysis with RnBeads: start analysis from Beta-values
Popular Question 14 months ago, created a question with more than 1,000 views. For abyss-fac: command not found on Kubuntu 14.04
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Tcga Data From Synapse: Whitelisting Criteria
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How To Compare Gene Expression And Methylation Level Of A Gene
Student 4.6 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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