phylochemistry
is a set of functions for chemical and genomic/transcriptomic analysis. These tools are provided though a combination of new functions and wrapped features of previously developed packages. A number of new functions to streamline analyses in this interdisciplinary space are also provided. This repository contains the latest version of the phylochemistry
R package.
phylochemistry
can be installed by following these four steps:
- Install
msa
andphangorn
by running the following code in R
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("msa")
BiocManager::install("ggtree")
BiocManager::install("phangorn")
BiocManager::install("seqinr")
BiocManager::install("Biostrings")
BiocManager::install("GenomicRanges")
- Install prequisite R packages by running the following code in R
install.packages("devtools")
install.packages("tidyverse")
install.packages("DT")
install.packages("RColorBrewer")
install.packages("xcms")
install.packages("data.table")
install.packages("rhandsontable")
install.packages("ape")
install.packages("ips")
-
(for Windows only) install RTools
-
(for Mac only) install XCode via the Mac AppStore
-
Restart R and install
phylochemistry
devtools::install_github("thebustalab/phylochemistry", quiet = FALSE, force = TRUE)
library(phylochemistry)
The phylochemistry
package is documented in this vignette.
- A Shiny app for GC-FID and GC-MS data analysis.
- Open reading frame extraction from multiple fasta files.
- Store BLAST results in a .csv file.
- Minor ticks for ggplot2 axes.
- Phylogenetic signal for discrete traits.
- Analyze multiple sequence alignments for sites associated with user-defined function
- Multiple column name, multiple row name data structures (aka "polylists").
- Draw annotated multiple sequence alignments.
- Use image analysis to automatically get the csv of a mass spectrum from a published image.
- Draw chemical structures in R from a csv of molecular coordinates.
- BLAST transcriptomes, via NCBI BLAST+.
- Multiple sequence alignments and codon alignments of amino acid and nucleotide sequences, via msa and orthologr.
- Phylogenetic tree construction (including g-blocks trimming, pruning, ancestral states reconstruction), via phangorn.
- Systematic read/write functions (csv, newick, wide tables, fasta, summary statistic tables, GFFs, chromatograms, mass spectra).
- Phylogenetic signal for continuous traits.