User: Vivek.b

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Vivek.b100
Reputation:
100
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Trusted
Location:
Germany
Website:
https://github.com/viv...
Twitter:
vivekbhr
Last seen:
7 months, 4 weeks ago
Joined:
4 years, 7 months ago
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v***********@gmail.com

Posts by Vivek.b

<prev • 38 results • page 1 of 4 • next >
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barcodeplot how to increase the font size
... Hi Everyone How do I increase the font size in limma barcodeplot? The manual says additional args are passed to the base `plot` function, and from there to base `par`, but I tried to use `lwd` and `cex` options and they didn't work. ``` barcodeplot(fit$t[,2], rnaseq$up, rna ...
limma written 8 months ago by Vivek.b100 • updated 8 months ago by Gordon Smyth39k
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Comment: C: CAGEr : problem while filtering the bamFile
... Hi It's been a while since I had this, but I think the problem was solved by switching the gene annotation to ensembl syle. ``` seqlevelsStyle(BSgenome.Mmusculus.UCSC.mm10) <- "ENSEMBL" ``` ...
written 8 months ago by Vivek.b100
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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 18 months ago by Vivek.b100
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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 18 months ago by Vivek.b100
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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 21 months ago by Vivek.b100
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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 22 months ago by Vivek.b100 • updated 22 months ago by Martin Morgan ♦♦ 24k
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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 2.7 years ago by Vivek.b100
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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 2.7 years ago by Vivek.b100 • updated 2.7 years ago by Aaron Lun25k
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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 3.3 years ago by Vivek.b100
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Comment: C: diffHiC differential HiC analysis starting from Ginteractions object
... Thanks Aaron. This works.. ...
written 3.3 years ago by Vivek.b100

Latest awards to Vivek.b

Popular Question 16 months ago, created a question with more than 1,000 views. For GOSEQ: could not find any categories for many genes
Popular Question 16 months ago, created a question with more than 1,000 views. For DESeq2 multi-factor comparison problem
Student 18 months ago, asked a question with at least 3 up-votes. For RDAVIDWebService Error 301: Moved Permanently
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Supporter 3.9 years ago, voted at least 25 times.
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