loom_too_Seurat: Read and process loom and H5AD files from FlyCellAtlas

In ipatop/FlyCellAtlas.download.with.annotations: Reads and process loom files from FlyCellAtlas to be compatible with Seurat

Read and process loom and H5AD files from FlyCellAtlas

Description

This function requires loom and h5ad files from FlyCellAtlas and process them into Seurat objects.

Usage

loom_too_Seurat(
  loom_file = "./loom/s_fca_biohub_body_wall_10x.loom",
  h5ad_file = "./loom/s_fca_biohub_body_wall_10x.h5ad",
  plot = T
)

Arguments

loom_file	character with Name and directory of loom file -h5da has to be in same directory-
h5ad_file	character with Name and directory of h5da file
plot	Boolean indicating if plots should be generated
dir	Directory to save RData and plots in

Value

Seurat object from paper without any further processing

Examples

There are examples in the folder names "./loom". To run it:
loom_to_seurat(loom_file = "~/Documents/scripts/FlyCellAtlas_download_with_annotations/loom/s_fca_biohub_body_wall_10x.loom")

ipatop/FlyCellAtlas.download.with.annotations documentation built on March 26, 2022, 1:46 a.m.