User: kevin.stachelek

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Posts by kevin.stachelek

<prev • 21 results • page 1 of 3 • next >
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Comment: C: multi-sample binary indexed coverage file format
... [genomicssqllite](https://github.com/mlin/GenomicSQLite) also seems like an interesting approach. Though it [doesn't have](https://mlin.github.io/GenomicSQLite/guide/) R bindings supported. ...
written 29 days ago by kevin.stachelek10
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Comment: C: multi-sample binary indexed coverage file format
... I also thought I could write genomicranges to an hdf5 file but it doesn't seem like there's a method for this in rhdf5? ...
written 4 weeks ago by kevin.stachelek10
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multi-sample binary indexed coverage file format
... I am using [wiggleplotr](https://bioconductor.org/packages/release/bioc/html/wiggleplotr.html) in a shiny app to visualize read coverage between sets of single cell bigwigs. I have chosen this solution because I cannot afford the memory requirments of loading read coverage into memory, rather specif ...
R rna-seq sequencing written 4 weeks ago by kevin.stachelek10
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Comment: C: sequence variant notation and formatting
... Thank you It is good to know that the first format is in accordance with HGVS Sequence variant nomenclature and that the second is a simplification. For reference I am using [MutationMapper][1] which relies on the simplified format which I am adapting for COSMIC data by just truncating the prelimi ...
written 5 months ago by kevin.stachelek10
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sequence variant notation and formatting
... I am trying to connect a database of sequence variants with information on dna and protein level changes to a tool that plots lollipop plots of those same variants. The database seems to use one protein variant notation and the plotting tool another. I would like to translate between the two, but do ...
snp sequencing written 5 months ago by kevin.stachelek10
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Comment: C: Exon density in uniform bins across bam files
... [this seems relevant][1] [1]: https://divingintogeneticsandgenomics.rbind.io/post/compute-averages-sums-on-granges-or-equal-length-bins/ ...
written 7 months ago by kevin.stachelek10
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Answer: A: Exon density in uniform bins across bam files
... using R `GenomicRanges` and given two granges objects `exonic_bed` and `bins` ``` hits <- GenomicRanges::findOverlaps(query = exonic_bed, subject = bins, ignore.strand = TRUE) overlaps <- pintersect(bins[subjectHits(hits)], exonic_bed[queryHits(hits)], ignore.strand = TRUE) subjecthits & ...
written 7 months ago by kevin.stachelek10
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Exon density in uniform bins across bam files
... I'd like to calculate the percent of bases that overlap exons in uniformly sized (n mB) windows across several bam files. Could anyone help me determine this preferably using bedtools or R? ...
alignment sequencing written 7 months ago by kevin.stachelek10
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Answer: A: Adjusting distance between chromosome ideograms in karyoplote R
... The ideogram is created by `plotKaryotype` which itself calls `kpAddCytobands` which calls `graphics::rect`. The linewidth argument `lwd` to this function was helpful for me to increase the spacing between chromosomes. It can modified at the level of `plotKaryotype` via ellipses. ...
written 9 months ago by kevin.stachelek10
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choice of reference genome when comparing counts of repetitive elements
... I am using [Tetranscripts][1] to identify changes in repetitive elements in exosome contents. I am concerned that the distribution and quantity of repetitive elements might be very different between reference genomes. Do you have any guidance on choosing an appropriate reference? premade gtf files a ...
genome written 9 months ago by kevin.stachelek10

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