Moderator: venu

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venu6.3k
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Posts by venu

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News: BioC2020: mark your calendars!
... BioC2020 will be held Wed July 29 - Fri July 31 in Boston, at Simmons University and Harvard Medical School. The website is up at https://bioc2020.bioconductor.org and will be undergoing frequent updates. Stay tuned for the announcement of invited speakers, registration and accommodations, calls for ...
bioc2020 news conference written 11 weeks ago by venu6.3k
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Comment: C: Different number of peaks between biological replicates?
... Hi, > THe H3K27ac is my experience is especially problematic as it always gives rather poor quality data. H3K4me1 is typically better (=more specific in terms of signal/noise ratio). Is there any reference for this statement? IMO, poor quality must depend on IP efficiency or antibody quality or ...
written 3 months ago by venu6.3k
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Answer: A: DiffBind to call differential binding of Super-enhancers from ROSE
... You can pass custom count matrix to diffBind (check [reference manual, page 3: Construct a DBA object][1]). - For each sample make a bed file of super enhancers - calculate read counts from all your BAM files (using deepTools multiBamSummary function) - pass this to diffBind [1]: https:// ...
written 3 months ago by venu6.3k
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Answer: A: Distribution of mutations in different parts of the genome
... This is called `topography of mutations`. There are not many papers on this aspect of the mutations. One way is to follow this [paper](https://www.nature.com/articles/ncomms11383). You will get more insights if you do mutational signature analysis first and do genome distribution of these signatures ...
written 5 months ago by venu6.3k
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Answer: A: Motif analysis from H3K27ac ChIPseq broad peaks
... If the signals in IGV are looking reasonable over background for ~10kb domains, it is totally acceptable. There are something called **Super-enhancers** which are minimum of 10-12kb in size with high H3K27ac signal. Just google the term, you'll find number of papers solely based on super-enhancers. ...
written 5 months ago by venu6.3k
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Comment: C: qsea - genomic annotation
... annotate the windows with [ChIPseeker][1] [1]: https://www.bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html#peak-annotation ...
written 6 months ago by venu6.3k
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Tool: R pakcage: ALPS - AnaLysis routines for ePigenomicS data
... From a recent experience of working with epigenomics data for several projects, I have realized there can be a lot of data analysis tasks that require lines of coding. I found myself repeating some of these tasks and thought it makes sense to put some of these functions under one roof. The result ...
dataviz R epigenomics tool written 6 months ago by venu6.3k
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Comment: C: bedGraphToBigWig : command not found
... Try this ./bedGraphToBigWig tl.bedgraph hg38.chrom.sizes tl.bw Also do this before trying above command, chmod +x /home/anatoly/Epigenetics/Internship/assignment/* Not sure your command `chmod`s all contents of the directory. ...
written 7 months ago by venu6.3k
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Comment: C: History of Biostars
... I'd guess, many basic questions are being asked over the previous years and answered very well, so with a simple google search, first hits are landing on biostars threads. Also *many* tool developers are documenting their tools with clean examples and responding to the user queries. Might be saturat ...
written 12 months ago by venu6.3k
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Comment: C: History of Biostars
... Aw, your title makes more sense. Yes, I will try to make per-year frequency of tags (a good idea to see troubled topics per year :p). ...
written 12 months ago by venu6.3k

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Popular Question 5 months ago, created a question with more than 1,000 views. For Human Genome Project: Twenty-five years of big biology
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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
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Commentator 12 months ago, created a comment with at least 3 up-votes. For C: perl code to extract sequences from multi-line fasta works on all test files but
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