GitHub - SilasK/CoDaSeq: Functions for compositional analysis of high throughput sequencing

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Functions for compositional analysis of high throughput sequencing

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Name		Name	Last commit message	Last commit date
Latest commit History 52 Commits
CoDaSeq		CoDaSeq
chunk		chunk
.DS_Store		.DS_Store
.gitignore		.gitignore
CoDaSeq.Rmd		CoDaSeq.Rmd
CoDaSeq.pdf		CoDaSeq.pdf
CoDaSeq_0.99.1.tar.gz		CoDaSeq_0.99.1.tar.gz
Intro_tiger_ladybug.Rmd		Intro_tiger_ladybug.Rmd
Intro_tiger_ladybug.pdf		Intro_tiger_ladybug.pdf
README.txt		README.txt
dols.R		dols.R
dols_2016.csv		dols_2016.csv
mean_var.pdf		mean_var.pdf
mean_var_Bayes.pdf		mean_var_Bayes.pdf
mean_var_relationship.R		mean_var_relationship.R
non_linear_barplot.R		non_linear_barplot.R
nonlinear_barplot.pdf		nonlinear_barplot.pdf
phi_cluster.pdf		phi_cluster.pdf
simple_biplot.R		simple_biplot.R
simple_biplot.pdf		simple_biplot.pdf
tongue_saliva.txt		tongue_saliva.txt
tongue_vs_cheek.txt		tongue_vs_cheek.txt

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This is the ongoing work to put together a complete suite of functions for CoDa analysis of microbiome, transcriptome and metagenome data

This is now an R package that can be installed by downloading it and running this command in your R console:

install.packages('devtools')
devtools::install_github('ggloor/CoDaSeq/CoDaSeq')

Alternatively (and you will need to install a lot of dependencies):
download the tar.gz file, then inside the R console type:
install.packages("path/to/CodaSeq_xxx.tar.gz", type="source", repos=NULL)

ak_op.txt are subsets of the HMP example dataset with attached keratinized gingiva and  supragingival plaque, there is an associated genera file as well . 

Other datasets will be added. There will be datasets for transcriptome, metagenome, selex and 16S rRNA gene tag sequencing