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Important Libraies After R Update

The document lists R packages to install for various types of analyses including forensic tools, DNA damage patterns, sequence analysis, plotting and data editing, color palettes, matrices and data frames, PCA and MDS, reading fasta files, and evolutionary analyses. It provides instructions to install over 50 packages through commands like install.packages and remotes::install_github to enable different analyses in R.

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MÉLIDA NÚÑEZ
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45 views3 pages

Important Libraies After R Update

The document lists R packages to install for various types of analyses including forensic tools, DNA damage patterns, sequence analysis, plotting and data editing, color palettes, matrices and data frames, PCA and MDS, reading fasta files, and evolutionary analyses. It provides instructions to install over 50 packages through commands like install.packages and remotes::install_github to enable different analyses in R.

Uploaded by

MÉLIDA NÚÑEZ
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as TXT, PDF, TXT or read online on Scribd
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########################################

# Important Libraies after R Update #


########################################

#check directory
getwd()
#Change directory
setwd("/Users/melidanunecastillo/Desktop")

##############
# R Notes #
##############

install.packages("rmarkdown")

###########################
# All package together #
###########################

# Forensic tools
install.packages(c("genepop", "genepi", "mixep", "forensic", "DNAtools",
"DNAseqtest", "dnapath"))

# DNA damage patterns aRchaic package


install.packages("remotes")
remotes::install_github("kkdey/aRchaic")

#####################
# Sequence analysis #
#####################

install.packages("seqinr")
install.packages("seqLogo")
install.packages("sequences")
install.packages("seqNet")

## Sanger analysis
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version='devel')
BiocManager::install("sangeranalyseR")

## BiocManager
install.packages("BiocManager")
## sangeranalyseR
install.packages("sangeranalyseR")

#########################################
# Plot and Data Edition libraries #
########################################

install.packages("plotly")
install.packages("ggplot2")
update.packages("ggplot2")
install.packages("ggmisc") # Scatter plot
install.packages("rgl")
yes
install.packages("devtools")
install.packages("carData")
install.packages("reshape2")
install.packages("dplyr")
install.packages("tidyverse")
install.packages("hrbrthemes")
install.packages("ggridges")
install.packages("ggplotlyExtra")
install.packages("ggpubr")
install.packages("ggstatsplot")
install.packages("gridExtra")
install.packages("ggrepel")
install.packages("gapminder") # Time series
install.packages("scales") # Time series
install.packages("tidyquant") # Enumerated Ticks with Tickvals and Ticktext with
plot_ly
install.packages("orca") #DEprecated(obsolete) plotly, Exporting Graphs as Static
Images in R
install.packages("processx") # join with plotly, Exporting Graphs as Static Images
in R
install.packages("kaleido") # Plotly, instead orca

#############################
# Color Paletts libraries #
#############################

install.packages("ColorPalette")
install.packages("paletteer")
install.packages("RColorBrewer")
display.brewer.all()
install.packages("viridis")
help("viridis_pal")
install.packages("rainbow")
install.packages("viridisLite")
install.packages("colorRamps")
install.packages("colorspace")
install.packages("ColorPalette")
install.packages("colorscience")
install.packages("colorspace")
# to call the funtion: pal <- choose_palette()

#############################
# Matrix and DF libraries #
#############################

install.packages("car")
install.packages("devtools")
install.packages("usethis")
install.packages("reshape2")

#############################
# PCA and MDS libraries #
#############################

install.packages("factoextra") # PCA
install.packages("corrplot") # PCA
install.packages("ade4 package") # PCA
install.packages("ExPosition") # PCA
install.packages("ExPosition package") # PCA
install.packages("FactoMineR") # PCA
install.packages("magrittr") # MDS
install.packages("stats") # MDS
yes
install.packages("MASS package") # MDS

###################################
# Fasta File reader libraries #
###################################

install.packages("seqinr")
install.packages("readr")
install.packages("sequences")

#############################
# Evolutionary libraries #
#############################
install.packages("ape")
install.packages("ade4")
install.packages(c("network", "NetworkInference", "NetworkComparisonTest",
"networkGen", "networktree", "networktools"))
install.packages("babette") # BEAST sofware
install.packages("bdskytools") # BEAST sofware
devtools::install_github("laduplessis/bdskytools")

install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")
install.packages("")

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