Vince Carey

Thanks for this submission. The package does not use any Bioconductor data structures. A GRanges instance would probably be useful for ``` head(results) #> chromosome repeat_length repeat_seq start end repeat_seq2...

How about the GenomicInteractions class? How about using DNAString to represent your sequences? Do you use Bioconductor with your data?

Hi, do you plan to work on interoperation of this package with Bioconductor? Please let us know.

I think the "Title" field in DESCRIPTION may be wrong.

Vignettes do not explain or give a reference to CosMx. Please give scientific role of the package/technology in the vignette introductions so that newcomers are given context.

Thanks for being so responsive. Now I feel we need to think about interoperability. ``` counts num [1:2198, 1:960] 0 0 0 0 0 0 0 0 0 0 ......

Thanks for this submission. This package will need some revision in order to enter the review process. - The `simulated_example` data is a list with a number of components; it...

Your README.md has "The goal of betAS is to ... This is a line from RStudio".

Please use a name other than "vignette.Rmd" for your vignette document. Please name the chunks in the vignette. Code like ``` bead

Thanks for this submission. Do not put a vector of numbers in your vignette ``` (echo=FALSE) betas