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Should be able to do both a small chromosome overview (as was implemented in Dalliance 0.7 and earlier), and an overview of _all_ chromosomes.
Does it make sense to share code between these two?
Ban…
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Can igv display chromhmm tracks such as the ones in this example
http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&non…
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There appears to be some debugging/testing code left in [Shiny\.addCustomMessageHandler\("fubar",](https://github.com/paul-shannon/igvShiny/blob/96d73672be10356e5dacc9a3df4b6be51fd69032/inst/htmlwidge…
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It would be convenient if JBrowse could render spliced alignments from tabix-indexed GFF3 files using the CIGAR string in the GFF3 Gap attribute (e.g., produced from gmap's gff3_match_est format), rat…
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I was able to install rbp-maps using Docker using the command `docker pull brianyee/rbp-maps:a5c9bd9` (but not `docker pull brianyee/rbp-maps`). However, I was not able to successfully run `plot_map` …
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For the dmr pipeline, it requires having to bgzip/tabix a pileup bed file. Is there a way to have modkit to automatically generate this as an option in the "pileup" command? Eg. --bgzip as an option i…
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I have been following the instructions on the docker hub (https://hub.docker.com/r/ave2/allelic-variation-explorer/) to input gff data in to the system.
First I get an error when running the bedToBig…
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The majority of bigwig/bigbed file format spec include the supplementary info which is https://www.ncbi.nlm.nih.gov/pubmed/20639541 and existing parser implementations
The supplementary info doc de…
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It is not clear from docs if pileup support chip-seq tracks (narrow/broad peaks files). If yes, then it would be nice to see an example if no, then it would nice to know if the feature is in plans?
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Just wanted to give you a heads up, the devel version of `rtracklayer` is failing on Bioc:
http://bioconductor.org/checkResults/devel/bioc-LATEST/rtracklayer/
Thanks!,
Brian