User: Leandro Lima

gravatar for Leandro Lima
Leandro Lima900
Reputation:
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Location:
San Francisco, CA
Website:
http://www.ime.usp.br/...
Twitter:
lelimat
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Google Scholar Page
Last seen:
1 day, 6 hours ago
Joined:
6 years, 6 months ago
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Bioinformatics Software Engineer at Gladstone Institutes

Posts by Leandro Lima

<prev • 92 results • page 1 of 10 • next >
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Answer: A: Genome Version Of Targetscan
... hg19. More info: http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi ...
written 3 months ago by Leandro Lima900
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Comment: C: List Of Genome Sequencing Centers/Institutes
... It looks like only the Google Maps link is working now. ...
written 7 months ago by Leandro Lima900
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Comment: C: How to use GRCh38 as reference for Annotating the variants using Annovar?
... This also might be helpful: https://www.biostars.org/p/196985/ ...
written 7 months ago by Leandro Lima900
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Answer: A: SnpMatrix from VCF file
... This should also work (I'm assuming that everything that is not 0/0, 0/1 or 1/1 should be considered as 0): vcf=genotypes.vcf vcftools --vcf $vcf --extract-FORMAT-info GT --out requiredFormat # Creating SNP.txt awk '{$1=$1":"$2; $2=""; print $0}' requiredFormat.GT.FOR ...
written 9 months ago by Leandro Lima900
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Answer: A: visualize CNV data based on WGS
... Hi, Bogdan. Have you tried [IGV][1]? You can load the BAMs and the BED files to check. Leandro [1]: http://software.broadinstitute.org/software/igv/ ...
written 11 months ago by Leandro Lima900
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Comment: C: Machine Learning/Deep Learning approaches to integrate genotype and annotation i
... Thanks for the link, Hussain. They use genotype information, but they are not using any annotation (e.g. functional impact, frequency, etc.). ...
written 11 months ago by Leandro Lima900
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Machine Learning/Deep Learning approaches to integrate genotype and annotation information for predictions?
... Hi, everyone. I'm looking for some material (papers/tools) showing approaches to integrate genotype information (e.g. from WGS) and the variant/gene annotations to do predictions (e.g. age of onset, phenotype) with ML/DL. Any recommendations? Thanks in advance, Leandro ...
annotation deep learning machine learning written 11 months ago by Leandro Lima900 • updated 11 months ago by Hussain Ather890
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Comment: C: ./ Vs "0/0" In Vcf Files
... This happens when there is more than one alternative allele. Suppose your reference is A and the most common alt. allele is C, but G and T can also occur. Then, AC -> 0/1 AG -> 0/2 AT -> 0/3 I believe this is common in indels. ...
written 12 months ago by Leandro Lima900
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Answer: A: Data retrieval from GEO
... I believe GEOmetadb could help you: https://gbnci-abcc.ncifcrf.gov/geo/gsm.php R package: http://bioconductor.org/packages/2.2/bioc/html/GEOmetadb.html ...
written 15 months ago by Leandro Lima900
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Comment: C: CNV frequencies and MAF
... Hi @smarini1. Sorry, but for now it's only possible to check for occurrence in a certain number of samples (and DGV gives this information), not the frequency. Leandro ...
written 22 months ago by Leandro Lima900

Latest awards to Leandro Lima

Student 3 months ago, asked a question with at least 3 up-votes. For CNV frequencies and MAF
Popular Question 4 months ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Popular Question 13 months ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Popular Question 22 months ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Popular Question 2.3 years ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Difference Between "Mate Pair" And "Pair-End"
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: 1000 Genomes Ld Calculation
Appreciated 4.4 years ago, created a post with more than 5 votes. For A: 1000 Genomes Ld Calculation
Good Answer 4.4 years ago, created an answer that was upvoted at least 5 times. For A: 1000 Genomes Ld Calculation
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Voter 4.7 years ago, voted more than 100 times.
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Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: What Is The Recommended Way To Use Bwa On Files Containing Haplotypes Of An Exom
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: What'S The Meaning Of "Random Walk" In The Gsea Paper Published By The Broad Ins
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: Need Recommendation On Good Tutorials For Performing Gwas
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: How To Visualize Custom 2D Genomic Data In A Genome Browser?
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Should I Start With Python 3?
Teacher 6.4 years ago, created an answer with at least 3 up-votes. For A: Gene Coexpression Networks

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