User: Bogdan

gravatar for Bogdan
Bogdan530
Reputation:
530
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Trusted
Location:
Palo Alto, CA, USA
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Google Scholar Page
Last seen:
41 minutes ago
Joined:
6 years ago
Email:
t*****@gmail.com

about me

Posts by Bogdan

<prev • 196 results • page 1 of 20 • next >
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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 31 minutes ago by Bogdan530
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Comment: C: single cell RNA-seq pipeline
... thank you Mike ! the list of available tools is very useful indeed ! ...
written 4 days ago by Bogdan530
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single cell RNA-seq pipeline
... Dear all, please would you advise about a single-cell RNA-seq pipeline to use, that is both robust/mature and user-friendly ? thank you very much ! -- bogdan ...
scrna-seq written 4 days ago by Bogdan530 • updated 4 days ago by Mike990
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Comment: C: Annotation for SV and CNV
... Please, would you let us know, does AnnotSV also infer fusions and truncations depending on gene orientation and SV orientation ? Thank you ! ...
written 4 days ago by Bogdan530
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(Closed) even display of unevenly spaced numbers on x/y coordinates
... Dear all, please would you advise on how I could make an even display of unevenly spaced number on a graph in R. For example, considering the code below : BREAKS = c(0, 0.1, 1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500) a <- seq(0,100,0.1) b <- seq(0,1000,0 ...
R written 6 days ago by Bogdan530
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visualization of chromatin interaction networks
... Dear all, please would you advise if there is any bioinformatics tool (in R/Bioc, or in any other environment eg Cytoscape) that could help with the visualization of CHROMATIN INTERACTION NETWORKS as a GRAPH (where NODES="chromosome loci", and EDGES = "interactions"). Thanks a lot ! -- bogdan ...
interactions networks chromosome written 14 days ago by Bogdan530 • updated 14 days ago by EagleEye5.5k
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about ECDF in ggplot2
... Dear all, I would appreciate having your advice/suggestions/comments on the following : 1 -- starting from a vector that contains the LENGTHS of DELETIONS (numerically, the values are from 1 to 10 000) 2 -- shall I display the ECDF by using the R code and some "limits" : **BREAKS = c(0, 10, ...
ggplot2 written 15 days ago by Bogdan530
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Comment: C: Assembling a sequence from the pairs of letters (X,Y)
... Thank you : yes, using transcripts() instead of genes() is a very good suggestion. Thanks ! ...
written 17 days ago by Bogdan530
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displaying graphs in R
... Dear all, please what package would you recommend for displaying the graphs in R (ideally, R packages with enhanced visualizations that also provide some graph-based algorithms). thank you, -- bogdan ...
networks graph written 17 days ago by Bogdan530
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Comment: C: Assembling a sequence from the pairs of letters (X,Y)
... Dear Daniel, as I do not have your email address, please may I post here a question about BioMart and StructuralVariantAnnotation. I am using the piece of R code below, that was inspired by the package StructuralVariantAnnotation that you have written in order to annotate the Structural Variants f ...
written 19 days ago by Bogdan530

Latest awards to Bogdan

Popular Question 4 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 4 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 4 months ago, created a question with more than 1,000 views. For "for loop" and AUTOPLOT function
Popular Question 4 months ago, created a question with more than 1,000 views. For estimating tumor purity and ploidy and CNV
Popular Question 4 months ago, created a question with more than 1,000 views. For about merging VCF files
Popular Question 5 months ago, created a question with more than 1,000 views. For about merging VCF files
Student 5 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 5 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
Popular Question 8 months ago, created a question with more than 1,000 views. For about merging VCF files
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to analyze RIP-seq data
Student 8 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 10 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 intersect VCF files
Popular Question 13 months ago, created a question with more than 1,000 views. For about xlim() in ggbio and CIRCLE layout
Centurion 15 months ago, created 100 posts.
Student 15 months ago, asked a question with at least 3 up-votes. For annotation of SV (Structural Variants)
Supporter 16 months ago, voted at least 25 times.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For about GRAnges and append
Scholar 2.2 years ago, created an answer that has been accepted. For A: Calculating fold change at enhancers and promoters

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