User: Bogdan

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Bogdan680
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Palo Alto, CA, USA
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Posts by Bogdan

<prev • 219 results • page 1 of 22 • next >
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Comment: C: normalization of ChIP-seq data
... Hi Devon, thank you. We do not have input DNA. ...
written 8 days ago by Bogdan680
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normalization of ChIP-seq data
... Dear all, please may I ask about your suggestions regarding the packages/methods that I could use for ChIP-seq normalization (shall I compare two ChIP-seq datasets : before_treatment, and after_treatment). thanks a lot ! -- bogdan ...
normalization chip-seq written 8 days ago by Bogdan680 • updated 8 days ago by Devon Ryan86k
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workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
... Dear all, any comments or suggestions regarding a pipeline "language"/ workflow management system to choose from in order to wrap up some data analysis pipelines on SGE/SLURM clusters ? among possible choices : -- Snakemake : https://snakemake.readthedocs.io/en/stable/ -- Ruffus : http://www.ruf ...
pipeline language written 19 days ago by Bogdan680 • updated 19 days ago by WouterDeCoster34k
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Answer: A: filtering the somatic variants
... Or : ########################################################### vcf <- readVcf("AML.vcf",genome="hg38") ###################################################################### ################################### FILTERING a VCF OBJECT : AF_AD_filters = fun ...
written 19 days ago by Bogdan680
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Answer: A: filtering the somatic variants
... A slightly modified version : ################################### FILTERING a VCF OBJECT : AF_AD_filters = function(x) { af <- geno(x)$AF[,"TUMOR"] >= 0.05 ad <- min(as(geno(x)$AD[,"TUMOR"], "List")) >= ...
written 19 days ago by Bogdan680
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Answer: A: filtering the somatic variants
... An example of filtering a VCF based on Allele Depth, Allele Fraction, FS, and SOR (metrics from GATK): AF_AD_filters = function(x) { af <- geno(x)$AF[,"TUMOR"] >= 0.05 ad <- min(as(geno(x)$AD[,"TUMOR"], "List")) >= ...
written 19 days ago by Bogdan680
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Comment: C: filtering the somatic variants
... yes, using VariantAnnotation package from BioC : https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html I could post an R script a bit later during the day .. ...
written 19 days ago by Bogdan680
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Comment: C: gene set enrichment analysis
... Thanks, Malcolm ! Just came across EnrichmentBrowser, that seems to have implemented lots of algorithms : https://bioconductor.org/packages/release/bioc/html/EnrichmentBrowser.html ...
written 5 weeks ago by Bogdan680
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Comment: C: gene set enrichment analysis
... Thanks a lot, Ram ! yes, we would like to include Webgestalt (preferably WebgestaltR) in our R computational pipeline. ...
written 5 weeks ago by Bogdan680
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Comment: C: gene set enrichment analysis
... Thank you very much for your suggestions. I have been looking into WebGestaltR documentation (https://cran.r-project.org/web/packages/WebGestaltR/WebGestaltR.pdf), and if I may ask, what is the simplest setup of the command "WebGestaltR" ? In the package manual, it is written : WebGestaltR(e ...
written 5 weeks ago by Bogdan680 • updated 5 weeks ago by RamRS19k

Latest awards to Bogdan

Popular Question 16 days ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 7 weeks ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 9 weeks ago, created a question with more than 1,000 views. For filtering VCF files
Appreciated 9 weeks ago, created a post with more than 5 votes. For sharing BiocWorkshops 2018
Popular Question 10 weeks ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 3 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 3 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 7 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 7 months ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
Popular Question 7 months ago, created a question with more than 1,000 views. For "for loop" and AUTOPLOT function
Popular Question 7 months ago, created a question with more than 1,000 views. For estimating tumor purity and ploidy and CNV
Popular Question 8 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 9 months ago, created a question with more than 1,000 views. For about merging VCF files
Student 9 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 9 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 11 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 12 months ago, created a question with more than 1,000 views. For about merging VCF files
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to analyze RIP-seq data
Student 12 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 14 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 16 months ago, created a question with more than 1,000 views. For intersect VCF files
Popular Question 17 months ago, created a question with more than 1,000 views. For about xlim() in ggbio and CIRCLE layout
Centurion 19 months ago, created 100 posts.
Student 19 months ago, asked a question with at least 3 up-votes. For annotation of SV (Structural Variants)
Supporter 20 months ago, voted at least 25 times.

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