install.packages("tidyverse")

install.packages("dplyr")
library(tidyverse)

install.packages("Seurat")
#> Error appeared so I tried to download the dependency "SeuratObject"

install.packages("SeuratObject")
#> Another error appeared so I tried to download the dependency "rgeos"

install.packages("rgeos")
#> Now somehow there is a configuration error...

install.packages("SeuratDisk")
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_github("mojaveazure/seurat-disk")

install.packages("hdf5r")

library(tidyverse)
library(Seurat)
library(SeuratDisk)

loom_obj <- Connect(filename = "first-trimester-decidua-human-placenta-10XV2.loom", mode = 'r')

(loom_obj[["matrix"]])


loom_obj[["row_attrs"]]

data <- as.data.frame(loom_obj[["col_attrs"]])

num_cols <- unlist(lapply(data, is.numeric)) 
num_cols

data_num <- data[ , num_cols] 
sort(colSums(data_num))

# Try to filter out the first five rows of the loom matrix
# Then filter out Emptydrop_IsCell
# As an alternative, use the Bioconductor package (go to scRNA-Seq Tutorial file)

library(here)
here("ff3365eb-8376-5613-b9a7-8bed5530c0fc", "c0d33f68-1573-45d2-9295-7f93f9a086b0.loom")
loom_obj1 <- Connect(filename = here("ff3365eb-8376-5613-b9a7-8bed5530c0fc", "c0d33f68-1573-45d2-9295-7f93f9a086b0.loom"), mode = 'r')

loom_obj1

seurat_loom <- as.Seurat(loom_obj)

getwd()
list.files()
installed.packages()