User: Vivek.b

gravatar for Vivek.b
Vivek.b50
Reputation:
50
Status:
New User
Location:
Germany
Website:
https://github.com/viv...
Twitter:
vivekbhr
Last seen:
3 weeks, 5 days ago
Joined:
3 years, 3 months ago
Email:
v***********@gmail.com

Posts by Vivek.b

<prev • 36 results • page 1 of 4 • next >
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Answer: A: VariantAnnotation::locateVariants error coming from XVector
... All right problem solved..! The update of S4Vectors from 0.17 to 0.19 (from GitHub) caused VariantAnnotation functions to break. Downgrading (using biocLite) solved it. ...
written 11 weeks ago by Vivek.b50
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VariantAnnotation::locateVariants error coming from XVector
... Hi all I have been getting the following error today on the files which worked fine yesterday :  Error: subscript is a NSBS object that is incompatible with the current subsetting operation Happened after I updated some bioconductor packages (don't remember which ones)   Reproducible example: ...
variantannotation iranges xvector written 11 weeks ago by Vivek.b50
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Comment: C: bplapply with ShortRead functions
... Thanks Martin. I think the issue was the second one you mentioned. Today I killed some processes on my computer and freed a few GBs of memory, and the function is now working. So it needed more memory when executed multi-core than on single core. Weird coincidence for me, yesterday I tried on our Rs ...
written 6 months ago by Vivek.b50
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bplapply with ShortRead functions
... Hey everyone I am facing an issue with using ShortRead functions with bplapply. I am trying to demultiplex a fastq file. Following is an example function, which does nothing but creates multiple paired-end fastq files, all containing same reads : demultiplex_fastq <- function(fastq_R1, fastq_R ...
shortread biocparallel written 6 months ago by Vivek.b50 • updated 6 months ago by Martin Morgan ♦♦ 22k
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Comment: C: csaw : effect of library size on filtering of uninteresting windows
... Got it.. Thanks Aaron.. I want you to keep doing your great job :) ...
written 17 months ago by Vivek.b50
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csaw : effect of library size on filtering of uninteresting windows
... Hi there, I am trying the csaw package to filter the background from my data using the "local enrichment" method. I first tested in a dataset with low input material (resulting in low library sizes) and find that the method works nicely, when I keep all regions with 2-fold enrichment over the local ...
csaw written 17 months ago by Vivek.b50 • updated 17 months ago by Aaron Lun20k
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Rsamtools filterBam question
... Hi Everyone I have two questions related to Rsamtools : 1. I am trying to filter my bam file by scanning the genome in 1kb bins, and removing reads that match certain criteria. But I will have to bin the genome chromosome by chromosome and run the filtering per chromosome.. I created the followin ...
rsamtools written 23 months ago by Vivek.b50
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Comment: C: diffHiC differential HiC analysis starting from Ginteractions object
... Thanks Aaron. This works.. ...
written 2.0 years ago by Vivek.b50
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Comment: C: diffHiC differential HiC analysis starting from Ginteractions object
... Hi Aaron Thanks for the reply. Using restriction frag size produced different bin sizes (since sometime i get a cut, sometimes not. plus they are different cell lines). But I now overcome this by using fixed bin size to create the matrix (not restriction frag length).  I can overcome #3 since I ha ...
written 2.0 years ago by Vivek.b50
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diffHiC differential HiC analysis starting from Ginteractions object
... Hi  I would like to use difHiC to get differential domains using two different cell lines. I have converted my normalized matrix for each of them into GInteraction objects.   ``` $s2 GInteractions object with 6398123 interactions and 1 metadata column: seqnames1 ranges1 ...
diffhic interactionset written 2.0 years ago by Vivek.b50

Latest awards to Vivek.b

Student 11 weeks ago, asked a question with at least 3 up-votes. For RDAVIDWebService Error 301: Moved Permanently
Popular Question 15 months ago, created a question with more than 1,000 views. For DEXSeq on FeatureCounts output
Popular Question 15 months ago, created a question with more than 1,000 views. For RDAVIDWebService Error 301: Moved Permanently
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