custom.db <- ("custom_db/GeneSet1/")
scGate_models_DB <- custom_db_scGATE(system.file("custom_db/GeneSet1/"))
scGate_models_DB <- custom_db_scGATE(("custom_db/GeneSet1/"))
suppressWarnings(source(system.file("scGATE","custom_df_scGATE.R",package = "STEGO.R")))
scGate_models_DB <- custom_db_scGATE(("custom_db/GeneSet1/"))
scGate_models_DB <- suppressWarnings(custom_db_scGATE(("custom_db/GeneSet1/")))
scGate_models_DB
scGate_models_DB <- suppressWarnings(custom_db_scGATE(("custom_db/GeneSet1/")))
suppressWarnings(source(system.file("scGATE","custom_df_scGATE.R",package = "STEGO.R")))
scGate_models_DB <- suppressWarnings(custom_db_scGATE(("custom_db/GeneSet1/")))
scGate_models_DB
suppressWarnings(source(system.file("scGATE","custom_df_scGATE.R",package = "STEGO.R")))
suppressWarnings(source(system.file("scGATE","custom_annotation_models.R",package = "STEGO.R")))
View(custom_db_scGATE)
getwd()
devtools::install_github("KerryAM-R/STEGO.R", force = T)
devtools::install_github("KerryAM-R/STEGO.R", force = T)
devtools::install_github("KerryAM-R/STEGO.R", force = T)
suppressWarnings(source(system.file("scGATE","custom_df_scGATE.R",package = "STEGO.R")))
(source(system.file("scGATE","custom_annotation_models.R",package = "STEGO.R")))
(source(system.file("OverRep","",package = "STEGO.R")))
(source(system.file("OverRep","GeneSet.csv",package = "STEGO.R")))
(source(system.file("OverRep","GeneSets.csv",package = "STEGO.R")))
(read.csv(system.file("OverRep","GeneSets.csv",package = "STEGO.R")))
STEGO.R::Load_required_packages()
STEGO.R::runSTEGO()
devtools::install_github("KerryAM-R/STEGO.R")
STEGO.R::Load_required_packages()
STEGO.R::runSTEGO()
devtools::install_github("KerryAM-R/STEGO.R")
devtools::install_github("KerryAM-R/STEGO.R")
STEGO.R::Load_required_packages()
STEGO.R::runSTEGO()
STEGO.R::Load_required_packages()
STEGO.R::runSTEGO()
if (!require("devtools", quietly = TRUE))
install.packages("devtools")
# installing STEGO.R
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
if (!require("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("KerryAM-R/STEGO.R")
STEGO.R::Load_required_packages()
STEGO.R::runSTEGO()
STEGO.R::Load_required_packages()
STEGO.R::runSTEGO()
devtools::install_github("KerryAM-R/STEGO.R")
STEGO.R::Load_required_packages()
STEGO.R::runSTEGO()
devtools::install_github("KerryAM-R/STEGO.R")
devtools::install_github("KerryAM-R/STEGO.R")
usethis::edit_r_environ()
STEGO.R::Load_required_packages()
STEGO.R::runSTEGO()
STEGO.R::runSTEGO()
devtools::install_github("KerryAM-R/STEGO.R")
STEGO.R::Load_required_packages()
STEGO.R::runSTEGO()
STEGO.R::runSTEGO()
remotes::install_version("Matrix", version = "1.6-1")
library(Matrix, lib.loc = "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library")
detach("package:Matrix", unload = TRUE)
library(Matrix, lib.loc = "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library")
# remotes::install_version("Matrix", version = "1.6-1")
# remotes::install_version("Seurat", version = "4.3.0")
devtools::install_github("KerryAM-R/STEGO.R")
# remotes::install_version("Matrix", version = "1.6-1")
# remotes::install_version("Seurat", version = "4.3.0")
devtools::install_github("KerryAM-R/STEGO.R")
remotes::install_github("KerryAM-R/STEGO.R", ref = "beta-version", force = T)
# use this to run STEGO.R
STEGO.R::runSTEGO()
?scGate_annotating
# install the beta-version of STEGO.R -----
remotes::install_github("KerryAM-R/STEGO.R", ref = "beta-version", force = T)
?scGate_annotating
require(STEGO.R)
?scGate_annotating
# install the beta-version of STEGO.R -----
remotes::install_github("KerryAM-R/STEGO.R", ref = "beta-version", force = T)
require(STEGO.R)
# use this to run STEGO.R
runSTEGO()
# alpha/gamma chain
clust.data.raw <- read.csv("1_ClusTCR/AG_Multi_ClusTCR.csv")
# Run this line to check that the files are found before proeeding to automate the preprocessing STEP 1.
preprocessing(downloadTCRex = F, downloadClusTCR = F,downloadSeurat = F,downloadTCR_Explore = F)
require(STEGO.R)
?ddply
?%>%
# once that you have made sure the files are in the correct format, all of tehm will download to their respective folders.
preprocessing(downloadTCRex = T, downloadClusTCR = T,downloadSeurat = T,downloadTCR_Explore = T)
# Run this line to check that the files are found before proceeding to automate the pre-processing STEP 1.
preprocessing(downloadTCRex = F, downloadClusTCR = F,downloadSeurat = F,downloadTCR_Explore = F)
require(STEGO.R)
# Run this line to check that the files are found before proceeding to automate the pre-processing STEP 1.
preprocessing(downloadTCRex = F, downloadClusTCR = F,downloadSeurat = F,downloadTCR_Explore = F)
devtools::install_github("KerryAM-R/STEGO.R", ref = "beta-version")
devtools::install_github("KerryAM-R/STEGO.R", ref = "beta-version")
require(STEGO.R)
# Run this line to check that the files are found before proceeding to automate the pre-processing STEP 1.
preprocessing(downloadTCRex = F, downloadClusTCR = F,downloadSeurat = F,downloadTCR_Explore = F)
require(STEGO.R)
preprocessing_10x(downloadTCRex = F, downloadClusTCR = F,downloadSeurat = F,downloadTCR_Explore = F)
# Run this line to check that the files are found before proceeding to automate the pre-processing STEP 1.
# the four files need to be stored in the sub-folder as: barcode, features, matrix and contig.
?preprocessing_10x
require(STEGO.R)
# Run this line to check that the files are found before proceeding to automate the pre-processing STEP 1.
# the four files need to be stored in the sub-folder as: barcode, features, matrix and contig.
?preprocessing_10x
source("~/Desktop/Directory_for_Project/Installing.R")
source("~/Desktop/Directory_for_Project/Installing.R")
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
if (!require("devtools", quietly = TRUE))
install.packages("devtools")
install.packages("devtools")
install.packages("usethis")
# install stego.R with Devtools
# if you get asked about installing from SOURCE, select NO.
# if asked about updating the packages, select either 0 for all, or 3 for none.
# this may need to be repeated to fix any issues ---
devtools::install_github("KerryAM-R/STEGO.R")
source("~/Desktop/Directory_for_Project/Installing.R")
source("~/Desktop/Directory_for_Project/Installing.R")
# under development - latest build, but may be unstable
devtools::install_github("KerryAM-R/STEGO.R", ref = "beta-version")
# under development - latest build, but may be unstable
devtools::install_github("KerryAM-R/STEGO.R", ref = "beta-version")
# under development - latest build, but may be unstable
devtools::install_github("KerryAM-R/STEGO.R", ref = "beta-version", force = T)
# install STEGO.R with Devtools
# if you get asked about installing from SOURCE, select NO.
# if asked about updating the packages, select either 1 for all, or 3 for none.
devtools::install_github("KerryAM-R/STEGO.R")
devtools::install_github("Tatvic/RGoogleAnalytics")
# install STEGO.R with Devtools
# if you get asked about installing from SOURCE, select NO.
# if asked about updating the packages, select either 1 for all, or 3 for none.
devtools::install_github("KerryAM-R/STEGO.R")
# the four files need to be stored in the sub-folder as: barcode, features, matrix and contig.
preprocessing_10x(downloadTCRex = F, downloadClusTCR = F,downloadSeurat = F,downloadTCR_Explore = F)
require(STEGO.R)
# the four files need to be stored in the sub-folder as: barcode, features, matrix and contig.
preprocessing_10x(downloadTCRex = F, downloadClusTCR = F,downloadSeurat = F,downloadTCR_Explore = F)
# install STEGO.R with Devtools
# if you get asked about installing from SOURCE, select NO.
# if asked about updating the packages, select either 1 for all, or 3 for none.
devtools::install_github("KerryAM-R/STEGO.R")
require(STEGO.R)
?automated_sc_filtering
?automated_sc_filtering()
automated_sc_filtering(dataset_type = "10x")
require(STEGO.R)
automated_sc_filtering(dataset_type = "10x")
require(STEGO.R)
automated_sc_filtering(dataset_type = "10x")
# install STEGO.R with Devtools
# if you get asked about installing from SOURCE, select NO.
# if asked about updating the packages, select either 1 for all, or 3 for none.
devtools::install_github("KerryAM-R/STEGO.R")
require(STEGO.R)
# if you have lots of files, we recommend you check the cut-offs for the filtering and then use this to automate the process.
STEGO.R::automated_sc_filtering()
require(STEGO.R)
# use this to run STEGO.R
runSTEGO()
usethis::edit_r_environ()
#### Step 3c. annotating Seurat object (human) -----
?scGate_annotating
# install STEGO.R with Devtools
# if you get asked about installing from SOURCE, select NO.
# if asked about updating the packages, select either 1 for all, or 3 for none.
devtools::install_github("KerryAM-R/STEGO.R")
# install STEGO.R with Devtools
# if you get asked about installing from SOURCE, select NO.
# if asked about updating the packages, select either 1 for all, or 3 for none.
devtools::install_github("KerryAM-R/STEGO.R")
require(STEGO.R)
# install STEGO.R with Devtools
# if you get asked about installing from SOURCE, select NO.
# if asked about updating the packages, select either 1 for all, or 3 for none.
# also run this line to check fo rupdates
devtools::install_github("KerryAM-R/STEGO.R")
dir.create("/Users/kerrymullan/Library/R/arm64/4.4/library", recursive = TRUE)
require(STEGO.R)
# use this to run STEGO.R
runSTEGO()
# import all of the fonts to your system. Will only need to be done the first time.
require(extrafont)
font_import()
fonts <- fonttable()
head(fonts)
# import all of the fonts to your system. Will only need to be done the first time.
require(extrafont)
font_import()
loadfonts()
fonts <- fonttable()
head(fonts)
# use this to run STEGO.R
runSTEGO()
require(STEGO.R)
require(STEGO.R)
# use this to run STEGO.R
runSTEGO()
# installing olga with system2
system2("python", args = c("-m", "pip", "install", "olga"))
preprocessing_bd_rap(downloadTCRex = F, downloadClusTCR = F,downloadSeurat = F,downloadTCR_Explore = F,shiny_server = F)
require(STEGO.R)
# Run this line to check that the files are found before proceeding to automate the pre-processing STEP 1.
# the four files need to be stored in the sub-folder as: barcode, features, matrix and contig.
preprocessing_10x(downloadTCRex = F, downloadClusTCR = F,downloadSeurat = F,downloadTCR_Explore = F,shiny_server = F)
preprocessing_bd_rap(downloadTCRex = F, downloadClusTCR = F,downloadSeurat = F,downloadTCR_Explore = F,shiny_server = F)
