User: geocarvalho

gravatar for geocarvalho
geocarvalho80
Reputation:
80
Status:
Trusted
Location:
Brazil/Recife
Twitter:
@geovcnt
Last seen:
1 week ago
Joined:
1 year, 9 months ago
Email:
g**********@outlook.com

Posts by geocarvalho

<prev • 19 results • page 1 of 2 • next >
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Answer: A: Annotation tool for cnvKit
... Hello Naomi, other options that I know: * [StructuralVariantAnnotation](https://github.com/PapenfussLab/StructuralVariantAnnotation) * [AnnotSV](https://academic.oup.com/bioinformatics/article/34/20/3572/4970516) - [website](http://www.lbgi.fr/AnnotSV/) And if you want to take data from different ...
written 12 days ago by geocarvalho80
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Comment: C: how to fix error in getGEO function?
... h.mon LOL, I still thinking that you're a Jedi here! Any chance we can talk by email or chat? ...
written 3 months ago by geocarvalho80
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Comment: C: how to fix error in getGEO function?
... Hello Mr. h.mon, sorry for that but I noticed that you're from Brazil. And I would like to know about your projects here, could you please send me an email? I can't see your email on your account on biostars :/ Best regards! ...
written 3 months ago by geocarvalho80 • updated 3 months ago by h.mon21k
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Answer: A: Bioinformatics workshop or training courses
... What I recommend https://edu.t-bio.info https://bioinformatics.ca ...
written 4 months ago by geocarvalho80
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Answer: A: Large deletions in exome sequencing data
... I have been collecting some papers about CNV analysis ([link](https://github.com/geocarvalho/sv-cnv-studies)). There is a topic about Whole Exome Sequencing (WES). Nowadays, I'm using Exomedepth+cnvScan. I'm also trying to add more callers to my pipeline. ...
written 5 months ago by geocarvalho80
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Answer: A: Identifying CNVs from targeted amplicon sequencing
... I have been collecting some papers about CNV analysis ([link](https://github.com/geocarvalho/sv-cnv-studies)). There is a topic about Amplicon sequencing (AS). Nowadays, I'm using **Exomedepth+cnvScan**. I tested CoNVaDING, but didn't have good results with my data. Now I'm testing VisCap. Cheers. ...
written 6 months ago by geocarvalho80
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Answer: A: Plotting common SNPs from four individual from a vcf file
... http://bioinformatics.psb.ugent.be/webtools/Venn/ I normally use it ...
written 9 months ago by geocarvalho80
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Answer: A: Packages/modules for CNV, Indels, SNPs analysis
... See this repository: # [ThousandVariantCallersRepo](https://github.com/deaconjs/ThousandVariantCallersRepo) ...
written 10 months ago by geocarvalho80
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Answer: A: R books with Quantitative Genetics examples?
... Books with bioinformatics content and R that I know: 1. [Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools](https://www.amazon.com.br/Bioinformatics-Data-Skills-Reproducible-Research/dp/1449367372) 2. [R Programming for Bioinformatics](https://www.crcpress.com/R-Pr ...
written 10 months ago by geocarvalho80
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Comment: C: vcfeval Error: No sample name provided but calls is a multi-sample VCF
... About your other comment. If you have a VCF with mulitple samples you must choose one at a time. For example: * For a header: `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_1 Sample_2 Sample_3` command: ``` ./rtg vcfeval --baseline=reference.vcf.gz --bed-regions=roi.bed -c merged_extra.vc ...
written 11 months ago by geocarvalho80

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Supporter 20 months ago, voted at least 25 times.

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