README.md

In rogerswt/wadeTools: Wade's Hodgepodge of Flow Cytometry Functions

wadeTools

Package version of my toolbox

Installing the package

devtools::install_github("rogerswt/wadeTools", build_vignettes = TRUE)

Purpose of this package

The wadeTools package is a collection of a wide variety of R functions that I've written over the years. They accomplish big or small tasks that I find that I do over and over again, so as in any software development work, it makes sense to write it once (carefully and with an eye towards re-useability) and use it often.

I had originally created a 'tools' directory which had task-specific subdirectories (e.g. visualization, compensation, transformation, etc.). Any time I found I had a function that seemed to have broader utility than just the project at hand, I dumped it into the tools hierarchy. Over time functions and categories accumulated. Mostly these had to do specifically with flow cytometry data processing, but a few didn't.

Cytomics Workshop participants

I've only recently turned this collection into a formal R package. Why? Because I wanted to share these tools with Cytomics Workshop participants - people who are interested in acquiring or honing skills in developing and applying advanced computational analysis methods for flow cytometry. In earlier iterations of the workshop I simply shared the tools directory. That's akin to dumping a box of random tools on the workbench and asking you to build a barn, with no a priori knowledge of what a plane, or a saw, or a chisel was used for, or how to use them. A package has several monumental advantages over this ad hoc approach to sharing code:

1. it's easy to distribute via Github,
2. it installs and loads just like any other R package,
3. each function is documented with a help page that shows its arguments and usage, and in many cases examples of its use,
4. it comes with this vignette - essentially a cook's tour of the package and how to get started with it.

Everyone else

That said, anyone is free to grab this package and use it, if you find it useful in your work. If you do, please drop me a note! If you use it in a publication, please acknowledge.

All

The current version, 0.3.2, is pre-alpha. There are likely to be bugs. I would very much appreciate any bug reports! Email below.

Cheers, Wade

Wade Rogers

Still Pond Cytomics

rogerswt/wadeTools documentation built on Feb. 16, 2023, 7:47 a.m.