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DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
Compiled on Apr 15 2022 08:45:18
Current date and time: Mon Aug 14 19:34:42 2023
Logical CPU cores: 4
Thread number set to 4
The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs
Existing .quant files will be used
A fast algorithm will be used to select the MS2 mass accuracy setting
Mass accuracy will be determined separately for different runs
Scan windows will be inferred separately for different runs

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$ docker run -it --rm -v $PWD/:/data/ proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses wine SkylineCmd.exe      
To access the command-line interface for Skyline you can use either SkylineRunner.exe or SkylineCmd.exe.

SkylineRunner.exe is a tiny shim executable less than 10 KB in size.  It requires a Skyline installation, performed with  
the self-updating web installers, on the computer on which SkylineRunner is run.  SkylineRunner simply starts a separate  
Skyline process running without any user interface, pipes the parameter options from the command-line to the running
Skyline instance, and prints output from its Skyline instance to the command console. You can still run multiple instances
of SkylineRunner and it will start multiple instances of Skyline. The Skyline instance started by SkylineRunner is
independent of any other instances that may already be running on the same machine.  It is not necessary to have a visible
instance of Skyline running on your computer for SkylineRunner to work.

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# From: https://stackoverflow.com/questions/68657341/how-can-i-update-google-colabs-python-version

! python --version
# version 3.7 as default

#install python 3.9
!sudo apt-get update -y
!sudo apt-get install python3.10

#change alternatives

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#!/bin/bash

# To use, save this script in the directory you want to clean,
# name it "clean_files.bash"
# open bash in the directory
# run $ bash clean_files.bash
# This will generate a list of all the deleted files.

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---
title: "SctreeSeuratWorkflow"
output: html_document
date: '2022-04-29'
---


```{r}
# Modified from https://satijalab.org/seurat/articles/pbmc3k_tutorial.html

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# Note that you need to install these packages beforehand

library(AnnotationDbi)
library(org.Hs.eg.db)
library(dplyr)
library(ggplot2)

files <- dir("./STAR", recursive = TRUE, pattern = "ReadsPerGene", full.names=TRUE)

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"""
from: https://www.kaggle.com/c/rsna-miccai-brain-tumor-radiogenomic-classification/discussion/252942
extracts the metadata of dicom files

Use as: python dicom_meta.py --dataset train --input ./input --output ./ --n_jobs

"""
import argparse
import os
import pydicom

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