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> install.packages("bedtools")

Also tried this with bedtoolsr. Is there a way to force install? I am using version R 4.2.2.

Warning in install.packages :
  package ‘bedtools’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
r2evans
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erman
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  • `deepTools` is a Python package. How have you installed that package for use in R? Regarding `bedtools`, if you install it and have it in your PATH, you can use the `bedr` package to access the tool set within R. – Seth May 10 '23 at 18:31
  • There are several bedtools wrapper, mostly found on and installed through https://www.bioconductor.org. I fear you have to decide which one you need and ideally describe what you want to do with it. – Andre Wildberg May 10 '23 at 18:34
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    It is certainly difficult to search for packages for the R language. I tend to use one or both of `"r"` (quotes required) or `CRAN` in my searches, where the latter will look in the official R repositories (not necessarily bioconductor, for instance). The use of quotes around a parameter in google search mandates that it be included in the results, so [`"cran" "bedtools"`](https://www.google.com/search?q="cran"+"bedtools") returns the `bedr` package at the top of the list, ymmv. – r2evans May 10 '23 at 18:35
  • @Seth I tried this install.packages("devtools") devtools::install_github("PhanstielLab/bedtoolsr", force = TRUE) library(bedtoolsr) and got error sh: bedtools: command not found Warning in value[[3L]](cond) : bedtools does not appear to be installed or not in your PATH. If it is installed, please add it to your PATH or run: options(bedtools.path = "/path/to/") ** testing if installed package can be loaded from final location sh: bedtools: command not found bedtools does not appear to be installed or not in your PATH. options(bedtools.path = "/path/to/") – erman May 10 '23 at 19:17
  • [This link](https://bioconductor.org/packages/release/bioc/html/HelloRanges.html) and more specificall [here](https://bioconductor.org/about/release-announcements/) have version-specific installation instructions. – L Tyrone May 11 '23 at 04:11

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