User: Bogdan

gravatar for Bogdan
Bogdan600
Reputation:
600
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Trusted
Location:
Palo Alto, CA, USA
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12 hours ago
Joined:
6 years, 2 months ago
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about me

Posts by Bogdan

<prev • 205 results • page 1 of 21 • next >
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clonal populations in cancer samples
... Dear all, please could you advise, what is a typical range of AF (allele fractions) of somatic mutations in the cancer samples in order to consider them clonal or sub-clonal ? Thank you ... -- bogdan ...
snp clone whole genome sequencing cnv cancer written 13 hours ago by Bogdan600 • updated 3 hours ago by Kevin Blighe28k
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computing the CNA in the cancer genomes
... Dear all, please may I ask for your opinion : when analyzing the somatic Copy Number Alterations (CNA) in the cancer genomes (based on whole genome sequencing data), would you recommend using (running) the CNA_calling algorithm : -- per **EACH CHROMOSOME** individually, or -- on **ALL CHROMOS ...
cna copy number cnv cancer written 13 days ago by Bogdan600 • updated 12 days ago by Kevin Blighe28k
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the closest gene to a breakpoint
... Dear all, please would you advise : given a list of chromosomes coordinates (i.e. BREAKPOINTS), and the list of genes promoters (i.e. TSS), shall I use R/BioC, how could I get the closest gene TSS to a BREAKPOINT ? which function shall I use ? I am looking for a similar function as closestBed in b ...
bedtools R written 24 days ago by Bogdan600 • updated 24 days ago by h.mon19k
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News: sharing BiocWorkshops 2018
... Hi all, as I have seen this resource prepared by Sean Davis, thought to share it : https://bioconductor.github.io/BiocWorkshops/index.html ...
deseq2 rna-seq news limma glimma edger written 25 days ago by Bogdan600 • updated 25 days ago by Pierre Lindenbaum112k
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Answer: A: visualization of the translocations on the vertical scale
... Dear Benat, thank you also for the example below that you have graciously shared ! png("example_oneline.png", width=1500, height=800) pp <- getDefaultPlotParams(plot.type=3) pp$data2height <- 50 kp <- plotKaryotype(cex=2, plot.type=3, plot.params = pp, labels.plotter = NULL ...
written 6 weeks ago by Bogdan600
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Comment: C: visualization of the translocations on the vertical scale
... Thanks a lot, Bernat ! It look fabulous ... I will get back to you soon ! ...
written 7 weeks ago by Bogdan600
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computing chromothripsis on cancer genomes
... Dear all, please would you advise if there is any package that computes the areas with chromothripsis, given the cancer genome data (i.e. either the lists of CNV, or DEL, DUP, INV, or starting from BAM files) ? Thank you ! -- bogdan ...
sv snp cnv cancer written 7 weeks ago by Bogdan600
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visualization of the translocations on the vertical scale
... Dear all, please would you advise if there is any package already built (possibly in R/BioC) that could help with the following data visualization : 1. we have a set of SNV, CNV, SV from many cancer samples 2. we would like to display **the SNV and the CNV** along the chromosome coordinates (o ...
genome sv snv cnv circos written 7 weeks ago by Bogdan600
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Comment: C: sorting a BAM file
... Thank you Philipp for your suggestion ! ...
written 8 weeks ago by Bogdan600
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sorting a BAM file
... Dear all, would you please advise: beside SAMTOOLS, PICARD or SAMBAMBA, is there any tool that you would recommend in order to sort a BAM based on read name ? It is a BAM file from EGA that contains cancer sequencing data, and when I do run PICARD SortSam, I am getting the following error (below), ...
bam sort written 8 weeks ago by Bogdan600 • updated 8 weeks ago by Philipp Bayer5.6k

Latest awards to Bogdan

Popular Question 14 hours ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 10 days ago, created a question with more than 1,000 views. For filtering VCF files
Appreciated 12 days ago, created a post with more than 5 votes. For sharing BiocWorkshops 2018
Popular Question 21 days ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 6 weeks ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 8 weeks ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 6 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 6 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 6 months ago, created a question with more than 1,000 views. For "for loop" and AUTOPLOT function
Popular Question 6 months ago, created a question with more than 1,000 views. For estimating tumor purity and ploidy and CNV
Popular Question 6 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 about merging VCF files
Student 7 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 7 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
Popular Question 10 months ago, created a question with more than 1,000 views. For about merging VCF files
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to analyze RIP-seq data
Student 10 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 12 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 14 months ago, created a question with more than 1,000 views. For intersect VCF files
Popular Question 15 months ago, created a question with more than 1,000 views. For about xlim() in ggbio and CIRCLE layout
Centurion 17 months ago, created 100 posts.
Student 18 months ago, asked a question with at least 3 up-votes. For annotation of SV (Structural Variants)
Supporter 19 months ago, voted at least 25 times.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For about GRAnges and append

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