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07_clean_AMY_2021.R
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library("SingleCellExperiment")
library("rafalib")
library("iSEE")
library("lobstr")
library("here")
library("whisker")
library("usethis")
library("withr")
library("rsconnect")
library("sessioninfo")
load(here("rdas", "revision", "regionSpecific_Amyg-n5_cleaned-combined_SCE_MNT2021.rda"), verbose = TRUE)
source(here("shiny_apps", "00_clean_functions.R"))
explore_sce_original(sce.amy)
# [1] "Dimensions:"
# [1] 33538 15177
# [1] "Number of unique cell names:"
# [1] 15138
# [1] "Repeated cell names:"
#
# AAATGGATCCCGTAAA-1 AACCAACGTATCGCGC-1 AACTTCTTCGCTCTAC-1 AAGTACCTCTTCTTCC-1
# 2 2 2 2
# ACTATTCCAGCCTATA-1 AGACCCGGTGGCCCAT-1 AGCTTCCGTTCAATCG-1 ATCGCCTGTGGTACAG-1
# 2 2 2 2
# ATGAAAGAGACACACG-1 ATTGTTCTCATGACAC-1 CAACAGTCAGTCCCGA-1 CAACCAACATCAGCGC-1
# 2 2 2 2
# CAACCTCGTTCTCACC-1 CAACCTCTCTGATTCT-1 CACAGGCCATTAAAGG-1 CAGTTCCTCTATTTCG-1
# 2 2 2 2
# CCCTCTCGTATCCCAA-1 CGATCGGTCGGCATAT-1 CGCCATTGTGCTGCAC-1 CGGACACCACGTACTA-1
# 2 2 2 2
# CGTAATGGTCACTCTC-1 CGTGAATAGACCGTTT-1 GAAGCGATCGGTAGAG-1 GAGGCAAGTCTCAGGC-1
# 2 2 2 2
# GATGAGGTCCCATACC-1 GCACGTGCAAGCTGTT-1 GCTACAACATGTAACC-1 GGACGTCTCTTCGGTC-1
# 2 2 2 2
# GGTAATCAGGATATAC-1 GTCACTCTCTCCCATG-1 TCAAGACCAAATGATG-1 TCACATTTCTCACTCG-1
# 2 2 2 2
# TCATCCGTCGATTGAC-1 TCCTAATTCGATAACC-1 TCCTTCTAGGTATTGA-1 TCGAAGTTCTTGCAAG-1
# 2 2 2 2
# TGGTTAGCAGTCAACT-1 TTCTGTACATCTATCT-1 TTCTTCCAGTTGCTCA-1
# 2 2 2
# [1] "Number of unique genes names:"
# [1] 33538
sce_small <- create_small_sce_2021(sce.amy)
# * 1.1673461 GB
# * 0.6082883 GB
dim(sce_small)
# [1] 33538 14039
colData(sce_small)
rowData(sce_small)
save_sce_small(sce_small, "AMY", prefix = "tran2021_")
save_cell_colors(cell_colors.amy, "AMY")
create_app(sce_small, "AMY", cellmarkers = cellmarkers_fig_s7_2021, prefix = "tran2021_")
withr::with_dir(here("shiny_apps", "tran2021_AMY"), source("deploy.R"))
## Reproducibility information
print('Reproducibility information:')
Sys.time()
proc.time()
options(width = 120)
session_info()
## For the portion done on the cluster. For deploying, check 06_clean_NAc_2021.R
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 4.1.0 Patched (2021-05-18 r80330)
# os CentOS Linux 7 (Core)
# system x86_64, linux-gnu
# ui X11
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz US/Eastern
# date 2021-07-28
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
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