I am wondering what is your tool of choice for making a powerful statistical analyses and beautiful publication-ready plots in case of genomic intervals overlays, usually starting with a two or more .bed files. In last few days I was playing with BedSect (https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00003/full), but would like to try also some alternatives :)
Thank you in advance, for your tips and tricks!
ارغب أن تكون الابحاث في مجال أختصاصي هو علوم التربية البدنية ولاسيميا التدريب والفسلجة الرياضية
GenomicRanges is an R package for representing and manipulating genomic intervals. When used with the rtracklayer R package and it, dealing with the BED data format is really convenient.
Please see https://bioconductor.org/packages/GenomicRanges
The bedtools are useful for manipulation bed files. It includes Intersectbed (https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html). For assessing the statistical significance of overlap, you may use OLOGRAM:
DOI: 10.1093/nargab/lqab114
DOI: 10.1093/bioinformatics/btz810
I also like to use GenomicRanges in R (GRanges and IRanges; all from the Bioconductor manager).
Super handy and fast.
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