User: Leandro Lima

gravatar for Leandro Lima
Leandro Lima960
Reputation:
960
Status:
Trusted
Location:
San Francisco, CA
Website:
http://www.ime.usp.br/...
Twitter:
lelimat
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 6 days ago
Joined:
8 years, 3 months ago
Email:
l********@gmail.com

A bioinformatician working with Machine Learning at Gladstone Institutes

Posts by Leandro Lima

<prev • 94 results • page 1 of 10 • next >
0
votes
4
answers
9.0k
views
4
answers
Comment: C: intersect VCF files
... For this final step (creating a VCF with the variants in both VCFs with the samples from both VCFs), is there any difference between using `bcftools merge` and `GATK CombineVariants`? ...
written 8 months ago by Leandro Lima960
0
votes
0
answers
561
views
0
answers
Job: Bioinformatician / Biostatistician (Gladstone Institutes - San Francisco, CA)
... Hi, everyone. We are looking for a Bioinformatician or Biostatistician to join the Bioinformatics Core (Institute of Data Science and Biotechnology) at Gladstone Institutes/UCSF. **Responsibilities** Provide bioinformatics and computational support to the world-class biomedical research conducted ...
ucsf next-gen job rna-seq statistics written 14 months ago by Leandro Lima960
0
votes
1
answer
1.6k
views
1
answers
Answer: A: Genome Version Of Targetscan
... hg19. More info: http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi ...
written 2.0 years ago by Leandro Lima960
0
votes
11
answers
29k
views
11
answers
Comment: C: List Of Genome Sequencing Centers/Institutes
... It looks like only the Google Maps link is working now. ...
written 2.4 years ago by Leandro Lima960
1
vote
1
answer
2.6k
views
1
answers
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 2.4 years ago by Leandro Lima960
3
votes
3
answers
5.4k
views
3
answers
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 2.5 years ago by Leandro Lima960
1
vote
5
answers
2.2k
views
5
answers
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 2.7 years ago by Leandro Lima960
0
votes
1
answer
675
views
1
answers
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 2.7 years ago by Leandro Lima960
1
vote
1
answer
675
views
1
answer
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 2.7 years ago by Leandro Lima960 • updated 2.7 years ago by Hussain Ather940
0
votes
2
answers
6.7k
views
2
answers
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 2.8 years ago by Leandro Lima960

Latest awards to Leandro Lima

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Should I Start With Python 3?
Scholar 14 months ago, created an answer that has been accepted. For A: How To Identify Large Arrangements And Transposable Elements In Ngs Data?
Popular Question 21 months ago, created a question with more than 1,000 views. For Existing methods to evaluate the performance of SV/CNV calling tools
Student 2.1 years ago, asked a question with at least 3 up-votes. For CNV frequencies and MAF
Popular Question 2.1 years ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Popular Question 2.9 years ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Popular Question 3.6 years ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Popular Question 4.1 years ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Commentator 4.3 years ago, created a comment with at least 3 up-votes. For C: Difference Between "Mate Pair" And "Pair-End"
Appreciated 5.0 years ago, created a post with more than 5 votes. For A: 1000 Genomes Ld Calculation
Appreciated 6.1 years ago, created a post with more than 5 votes. For A: 1000 Genomes Ld Calculation
Good Answer 6.1 years ago, created an answer that was upvoted at least 5 times. For A: 1000 Genomes Ld Calculation
Voter 6.5 years ago, voted more than 100 times.
Supporter 6.5 years ago, voted at least 25 times.
Autobiographer 6.5 years ago, has more than 80 characters in the information field of the user's profile.
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Teacher 7.4 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 7.4 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 7.5 years ago, created an answer with at least 3 up-votes. For A: Need Recommendation On Good Tutorials For Performing Gwas
Teacher 7.6 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 7.7 years ago, created an answer with at least 3 up-votes. For A: Should I Start With Python 3?
Teacher 8.2 years ago, created an answer with at least 3 up-votes. For A: Gene Coexpression Networks

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 999 users visited in the last hour