velocessor

The pre-release version of the package can be pulled from GitHub using the devtools package:

install.packages("BiocManager") # from CRAN
BiocManager::install("trichelab/velocessor")

Super quickstart

0. Ram everything through Salmon/Alevin and tximeta

See the Alevin velocity tutorial for more details on this.

1. Load annotations

library(AnnotationHub)
ah <- AnnotationHub()
# query(ah, c("ensdb", "Ensembl 99", "Homo sapiens") )
ens99 <- ah[["AH78783"]]
gencode33 <- genes(ens99, columns=c("symbol", "gene_biotype"))

2. Load quantifications

library(velocessor)
alevin_suffix <- "_alevin"
runs <- list.files(pattern=paste0(alevin_suffix, "$"))
names(runs) <- sub(alevin_suffix, "", runs)
qm <- "alevin/quants_mat.gz"
txstub <- "gencode.v33.annotation.withintrons.expanded"
txis <- process_velo_txis(runs, txstub, anno=gencode33, 
                          HARMONY=TRUE, SCVELO=TRUE, 
                          BPPARAM=MulticoreParam(3))

3. Plot the results (optionally on rescaled axes)

txis <- rescale_dimred(txis, "UMAP") 
plot_velo(txis, embed="scaled_UMAP", sizeref=3)

4. Explore the results

plot_velo generates an interactive plot colored by velocity pseudotime by default (above) .

Try zooming in and out with the middle mouse button, hovering, and rotating.

For developers

The repository includes a Makefile to facilitate some common tasks.

Running tests

$ make test. Requires the testthat package. You can also specify a specific test file or files to run by adding a "file=" argument, like $ make test file=logging. test_package will do a regular-expression pattern match within the file names. See its documentation in the testthat package.

Updating documentation

$ make doc. Requires the roxygen2 package.