User: endrebak852

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endrebak85290
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Posts by endrebak852

<prev • 7 results • page 1 of 1 • next >
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Tool: New ultraperformant version of SICER/epic: epic2
... New version of the popular ChIP-Seq caller SICER out. See https://github.com/biocore-ntnu/epic2 for more. **Performance:** ![enter image description here][1] [1]: https://github.com/biocore-ntnu/epic2/raw/master/graphs/speed_epic2_vs_SICER_no_bigwig.png **CLI:** usage: epic2 [-h] [--tre ...
chip-seq tool written 12 weeks ago by endrebak85290
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Comment: C: Split a GRanges into one GRanges per chromosome/strand pair and put in GRangesLi
... Then I cannot do RleList1 - RleList2, but thanks :) ...
written 12 weeks ago by endrebak85290
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Split a GRanges into one GRanges per chromosome/strand pair and put in GRangesList?
... I want to find the coverage for each chromosome/strand pair, but unfortunately, the coverage-function takes no ìgnore.strand=FALSE` argument. Therefore I want to split a GRanges into the constituent chromosome/strand pairs and run coverage on the GRangesList. How do I do that? Example data: li ...
genomicranges written 12 weeks ago by endrebak85290 • updated 12 weeks ago by ATpoint13k
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How do I find the set of a genomicrange? (same as union(gr, gr))
... library(GenomicRanges) gr0 <- GRanges(Rle(c("chr2", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)), IRanges(1:10, width=10:1)) union(gr0, gr0) # GRanges object with 3 ranges and 0 metadata columns: # seqnames ranges strand # # [1] chr2 [1, 10] * ...
R bioconductor genomicranges written 12 weeks ago by endrebak85290 • updated 12 weeks ago by Michael Dondrup45k
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How do I subset a GRanges on chromosome, region and strand?
... library(GenomicRanges) gr=GRanges(seqnames=c("chr1","chr2","chr2"), ranges=IRanges(start=c(50,150,200),end=c(100,200,300)), strand=c("+","-","-") ) I want to get all intervals between 200-300 on chromosome 2, the minus strand. How do I do that? gr[seq ...
R bioconductor genomicranges written 12 weeks ago by endrebak85290 • updated 12 weeks ago by Bastien Hervé3.3k
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Comment: C: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
... That is one of the disadvantages of pull-based systems. But it has advantages over push-based systems also. I have workflow where I need to dl/process large amounts of data. Then Snakemake's tempfile capabilities are a godsend. To safely delete files, you need to know the DAG. ...
written 3 months ago by endrebak85290
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Answer: A: Can I read chrom, strand, pos, len from bam files without htslib?
... My solution. Works, but probably not the cleverest. Hinges on users having conda w/appropriate libs installed: # In setup.py from subprocess import check_output conda_path = check_output("which conda", shell=True).decode().strip() conda_include = [] conda_lib = [] ...
written 3 months ago by endrebak85290

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