User: nick

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nick70
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Posts by nick

<prev • 16 results • page 1 of 2 • next >
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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 10 weeks ago by nick70 • updated 10 weeks ago by rayoub80
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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 8 months ago by nick70
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Answer: A: TCGAquery function from TCGAbiolinks
... Have you tried with`GDCquery`? ...
written 10 months ago by nick70
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Comment: C: DNA methylation analysis with RnBeads: start analysis from Beta-values
... Yes, sorry I didn't specify that. ...
written 23 months ago by nick70
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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 23 months ago by nick70 • updated 23 months ago by andrew.j.skelton734.8k
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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 2.8 years ago by nick70 • updated 2.8 years ago by Jautis240
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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 3.3 years ago by nick70
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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 3.3 years ago by nick70
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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 3.5 years ago by nick70
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Comment: C: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Ge
... OK, thank you very much for the quick and comprehensive reply. ...
written 3.6 years ago by nick70

Latest awards to nick

Popular Question 10 weeks ago, created a question with more than 1,000 views. For DNA methylation analysis with RnBeads: start analysis from Beta-values
Popular Question 8 months ago, created a question with more than 1,000 views. For abyss-fac: command not found on Kubuntu 14.04
Popular Question 22 months ago, created a question with more than 1,000 views. For Tcga Data From Synapse: Whitelisting Criteria
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How To Compare Gene Expression And Methylation Level Of A Gene
Student 4.1 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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