Samuel Gamboa

@Kayla-Morrell, thank you! I've made the requested updates to the package. Please see below: Updates: + LazyData was set to false in the DESCRIPTION file. This required the addition of...

@Kayla-Morrell, thank you!

@lshep, we have published our data on [zenodo](https://zenodo.org/records/10980813) and use it as the default option in our [main function](https://github.com/waldronlab/bugphyzz/blob/7e3d6a7af247ed3594e394d0d43755d8811083db/R/bugphyzz.R#L56-L58). A couple of functions still use data from external sites. [One...

I made some comparisons of lefse with different platforms (conda, galaxy, and R). The results (features reported as significant) highly overlap, but a few more features were reported as significant...

@lshep, I added an abstract to the vignette and expanded the introduction to describe the package in more detail. I explain how the package should fit within Bioconductor workflows and...

@lshep, yes. Thanks for following up. I've already made the required changes. I'll bump the version today.

@lshep, I think there could be some issues with the connection on nebbiolo2 (Ubuntu). I keep getting an error when building the vignette or running the tests of the package....

Dear @DarioS, Thank you for your feedback. I think I've addressed all of the requested changes below: >+ Inconsistent use of camelCase and snake_case coding. For example, makeSignatures, importBugphyzz, force_download,...

One of the features of lefse-conda is determining which clades are differentially abundant. For example [this result](https://github.com/waldronlab/MicrobiomeBenchmarkDataLefse/blob/712fe691ff7130e16b16640f2ca732988d9ddb37/inst/extdata/gingivalplaque_a0.01_w0.01_lda3_it10_bp130.res#L1626). This clade was created by the lefse program. I think the abundance of...

Added a PR #59 with a function for plotting histograms of relative abundance.