Port over quietT/BCRgenes()

[Qile0317]

copies over the quietTCRgenes() and quietBCRgenes() functions from Trex and Ibex, and also adds a function quietVDJgenes() that runs both as a convenience. Lastly, some small changes are that all instances of the github checkout action has been upgraded to v4 from v3, and some redundant imports in DESCRIPTION have been trimmed.

[Qile0317]

@ncborcherding In the future when this version goes into the main bioconductor server, the sourcecode for those functions in Ibex and Trex can be removed and they can re-export those functions instead.

[Qile0317]

@ncborcherding Ensure the new changelog info I added are in the correct location in NEWS.md?

[ncborcherding]

@Qile0317 I don't think we can have functions that depend on Seurat - it is a massive dependency hole. I would prefer keeping everything to SeuratObject. Maybe we can keep the quiet functions and not have an independent variable gene function?

[Qile0317]

@Qile0317 I don't think we can have functions that depend on Seurat - it is a massive dependency hole. I would prefer keeping everything to SeuratObject. Maybe we can keep the quiet functions and not have an independent variable gene function?

@ncborcherding Right - so in this configuration Seurat is actually in Suggests and nothing from Seurat is actually loaded or imported. Rather the namespace is required to be loaded at runtime instead of package build time. Everything that was prefixed with Seurat:: is lazy loaded here and the variable gene filtering method would never have dispatched to the Seurat S3 method if a seurat object made from a presumably loaded Seurat package is already loaded. But I also understand the concern about Seurat as a "soft" dependency, so let me know if you'd still prefer to not have it and I'll remove it.

[ncborcherding]

@Qile0317

Think we need to drop it as that is not in keeping with Bioconductor policy and they also want equal support for SingleCellExperiment. Lets just do the quiet() functions.

Thanks,
Nick

[Qile0317]

Ok, sounds good, will remove now.