preprocess-exercise's Introduction

preprocess-exercise

Preprocessing tutorial for bioinformatics intermediate

Requirements in my environment

Bash: GNU bash, version 3.2.57(1)-release (x86_64-apple-darwin19)
Anaconda: 4.9.0

Precedure to create the conda environment

conda create -n r-4.0 --file envs/myenv.yaml

envs/myenv.yaml was created by the following steps:

conda create -y -n r-4.0 r=4.0
conda activate r-4.0
conda config --add channels r
conda config --add channels conda-forge
conda config --add channels bioconda
conda install -y -c conda-forge snakemake
conda install -y -c conda-forge jupyter
conda install -y -c conda-forge jupyterlab
conda install -y -c conda-forge papermill
conda install -y -c r r-irkernel
conda install -y -c conda-forge r-tidyverse
conda install -y -c conda-forge r-ggbeeswarm
conda install -y -c conda-forge r-shiny
conda install -y -c conda-forge r-plotly
conda install -y -c conda-forge r-ggally
conda install -y -c conda-forge r-pairsd3
conda install -y -c conda-forge r-ggpairs
conda install -y -c conda-forge r-rtsne
conda install -y -c conda-forge r-uwot
conda install -y -c conda-forge r-lintr
conda install -y -c conda-forge r-formatr
conda install -y -c conda-forge r-styler
conda install -y -c conda-forge r-markdown
conda install -y -c conda-forge r-knitr
conda install -y -c bioconda bioconductor-singlecellexperiment
conda install -y -c bioconda bioconductor-scater
conda install -y -c bioconda bioconductor-schex
conda install -y -c bioconda bioconductor-isee
conda install -y -c bioconda bioconductor-s4vectors
conda install -y -c bioconda bioconductor-biocstyle
R -e "IRkernel::installspec()"
mkdir -p envs
conda env export > envs/myenv.yaml