MicrobiomeBioinformaticsAnalysisWorkshop2023/PackageInstallation at main · monaparizadeh/MicrobiomeBioinformaticsAnalysisWorkshop2023 · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
# Package installation ####

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager") # Installs BiocManager, a package that facilitates the download of packages from the BioConductor repository.

# DADA2 to model the errors introduced during amplicon sequencing, and use that error model to infer the true sample composition (Callahan et al., 2016)
BiocManager::install("dada2")

# phyloseq to store all sequencing-related data as single experiment-level object and simplify analyses (McMurdie & Holmes, 2013)
BiocManager::install("phyloseq")

# vegan for ecological statistical functions (Oksanen et al., 2020)
install.packages("vegan")

# ggplot2 for plotting (Wickham, 2016)
install.packages("ggplot2")

# tidyverse for tidier coding (Wickham et al., 2019)
install.packages("tidyverse")

# tidyr to create tidy data (Wickham et al., 2023)
install.packages("tidyr")

# dyplr package for data manipulation (Wickham et al., 2014)
install.packages("dyplr")

# BiocGenerics for variance stabilizing transformatiom (Huber et al., 2015)
BiocManager::install("BiocGenerics")

# SummarizedExperiment for variance stabilizing transformatiom (Morgan et al., 2022)
BiocManager::install("SummarizedExperiment")

# rstatix for pipe friendly statistical analysis (Kassambara, 2021)
install.packages("rstatix")

# DESeq2 for differential abundance analysis (Love et al., 2014)
BiocManager::install("DESeq2")

# ggpubr for plotting statistics from rstatix (Kassambara, 2023) az
install.packages("ggpubr")

# RColorBrewer for ggplot color palettes (Neuwirth, 2022)
install.packages("RColorBrewer")

# gridExtra to arrange multiple grid-based plots (Chapman & Hall, 2005)
install.packages("gridExtra")