Wang-Cankun

// npm install jimp
const Jimp = require('jimp')

const outputSizes = [
  { name: 'android-chrome-192x192.png', width: 192, height: 192 },
  { name: 'android-chrome-512x512.png', width: 512, height: 512 },
  { name: 'apple-touch-icon.png', width: 180, height: 180 },
  { name: 'favicon-16x16.png', width: 16, height: 16 },
  { name: 'favicon-32x32.png', width: 32, height: 32 },
  { name: 'favicon.ico', width: 32, height: 32 },

Wang-Cankun

source(file.path(Sys.getenv("LMOD_PKG"), "init/R"))
module("load", "gnu/11.2.0")
old_ld_path1 <- Sys.getenv("LD_LIBRARY_PATH")
Sys.setenv(LD_LIBRARY_PATH = paste(old_ld_path1, "/apps/hdf5/gnu/9.1/openmpi/4.0/1.12.0/lib",sep=":"))
remotes::install_github("mojaveazure/seurat-disk")

Wang-Cankun

mean.fxn <- function(x) {
  return(log(x = rowMeans(x = x) + 1, base = 2))
}

calDR <-
  function(RAS_C1,
           graph.out,
           FindALLMarkers = T,
           lfcThres = 0,
           ident.1 = 1,

Wang-Cankun

 # Login as root
 sudo su -
 
 #libnsl.so.1: not found:
 yum install libnsl
 
 #gdal
 conda install -c conda-forge gdal
 
 #R

Wang-Cankun

# 1. Start an Rstudio serssion using your R specified version

# 2. In Rstudio, install hdf5r
source(file.path(Sys.getenv("LMOD_PKG"), "init/R"))
module("load", "gnu/9.1.0 hdf5-serial/1.12.0")
install.packages("hdf5r")

# 3. If you can load hdf5r in terminal but failed in R studio, run this before loading 
dyn.load('/apps/hdf5/gnu/9.1/openmpi/4.0/1.12.0/lib/libhdf5_hl.so.200')
library(hdf5r)

Wang-Cankun

Other      5 hrs 54 mins  ██████████▍░░░░░░░░░░  49.8%
Vue.js     5 hrs 42 mins  ██████████░░░░░░░░░░░  48.1%
Bash       11 mins        ▎░░░░░░░░░░░░░░░░░░░░   1.6%
Markdown   1 min          ░░░░░░░░░░░░░░░░░░░░░   0.2%
Python     0 secs         ░░░░░░░░░░░░░░░░░░░░░   0.1%

Wang-Cankun

library(here)
library(tidyverse)
library(jsonlite)

# For SEO: How to extract data from 10X web_summary.html using R
# A big JSON variable is at "web_summary.html" line 13
# raw_lines[13]
raw_lines <- read_lines("web_summary.html")

web_summary_json <-

Wang-Cankun

Error: run tensorboard failed in OSC jupyter notebook

%tensorboard --logdir lightning_logs

ERROR: Failed to start `tensorboard`: [Errno 13] Permission denied:
'tensorboard'

Solution:

Wang-Cankun

# Change /users/PAS1571/wangcankun100/R/tmp/ to your R temporary directory
tempdir <- function() "/users/PAS1571/wangcankun100/R/tmp/"
unlockBinding("tempdir", baseenv())
utils::assignInNamespace("tempdir", tempdir, ns="base", envir=baseenv())
assign("tempdir", tempdir, baseenv())
lockBinding("tempdir", baseenv())
#in order to make sure install.packages uses the custom temporary directory, one needs to do
Sys.setenv(TMPDIR="/users/PAS1571/wangcankun100/R/tmp/")