R package containing functions useful for stitching Visium capture areas. Related to the example human brain data described at http://research.libd.org/visiumStitched_brain/.
At https://research.libd.org/visiumStitched/reference/build_spe.html, the argument reference_gtf is not really explained. You should mention that if you are working on the same computer system where the GTF file for running SpaceRanger exists, that it'll be found automatically.
On the examples code, mention that we don't have that SpaceRanger GTF and we will thus use Gencode V32 because it's one of the closest GTFs to the actual one (name the version) that was used for the SpaceRanger run.
At https://research.libd.org/visiumStitched/reference/build_spe.html, the argument
reference_gtfis not really explained. You should mention that if you are working on the same computer system where the GTF file for running SpaceRanger exists, that it'll be found automatically.On the examples code, mention that we don't have that SpaceRanger GTF and we will thus use Gencode V32 because it's one of the closest GTFs to the actual one (name the version) that was used for the SpaceRanger run.