[Feature Request] Re-export / migration of quiet[BT]CRgenes() & alternative quieting method

[Qile0317]

@ncborcherding I feel that it may make more sense to either re-export or migrate the Trex and Ibex quiet[BT]CRgenes functions to scRepertoire, since this is much more known so people would likely have a higher chance of finding this functionality.

Additionally, I also think the following alternative may be superior than simply removing variable genes after already running FindVariableFeatures:

1. get the assay object of interest as a copy
2. for all rows on the assay copy that correspond to features that shouldn't factor into the VariableFeatures calculation, set them to 0
3. run seurat's findvariablefeatures
4. set the variable features vector of the actual assay itself to the result of 3, and discard the assay copy

I believe that the advantage here is that Seurat is further able to use less variable but still potentially relevant features that were originally ranked below the filtered features - in some cases this may help with excessive features being removed without needing to re-run FindVariableFeatures with a larger nFeatures argument.

Let me know what you think and I can PR immediately. Here is an example of what the function body could look like:

contigGenes <- rownames(seuratObject) %>%
    Ibex::quietBCRgenes() %>%
    Trex::quietTCRgenes()
contigGeneIndices <- which(rownames(seuratObject) %!in% contigGenes)

VariableFeatures(seuratObject) <- GetAssay(seuratObject, "RNA") %>%
    GetAssayData() %>%
    setRow(contigGeneIndices, 0) %>%
    CreateAssayObject() %>%
    FindVariableFeatures(
        selection.method = "mean.var.plot",
        nfeatures = 2000,
        mean.cutoff = c(0.1, Inf),
        dispersion.cutoff = c(0.5, Inf)
    ) %>%
    VariableFeatures()
seuratObject

[ncborcherding]

I think this makes sense - Ibex and Trex rely on data that has been formatted with scRepertoire, so dependencies wouldn't be an issue.

[Qile0317]

@ncborcherding Great - theres a few details I'm still considering but I'll PR a preliminary version in all 3 repos.