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RAM (version 1.2.0)

R for Amplicon-based Metagenomics

Description

This package provides a series of functions to make amplicon-based metagenomic analysis more accessible, and publication-quality plots simple. Amplicon-based (or targeted) metagenomics amplifies and sequences selected DNA regions of environmental samples, but not the entire pool of genetic material, which is referred to as shotgun metagenomics. The amplicon-metagenomics mainly aims at characterizing broad microbiota biodiversity in different environments.

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Version

Install

install.packages('RAM')

Monthly Downloads

23

Version

1.2.0

License

MIT + file LICENSE

Maintainer

Wen Chen

Last Published

December 10th, 2014

Functions in RAM (1.2.0)

Taxa.ord

Ordination Plot For Taxa Groups Using CCA or RDA Analysis
filter.META

Select METADATA Variables
core.OTU

Summary Of Core OTUs
shared.Taxa

Summary of Shared Taxa Across ALL Subjects
fread.OTU

Fast Load Large OTU Table
top.groups.plot

Plot the Top Taxon Groups
RAM.factors

Factor Formatting for RAM
RAM.plotting

Creating Plots with RAM
RAM.input.formatting

Data Input Formatting
assist.ordination

Perform CCA and RDA Analysis for OTU Tables
meta

Sample Metadata for ITS1/ITS2
tax.abund

Aggregate OTU Data Based on Taxonomy
LCA.OTU

Lowest Common Ancestor (LCA) OF EACH OTU
group.rich

Barplot Of Richness For Each Level Of A Given Metadata Variable
group.spec

Boxplot Of Richness For Each Level Of A Given Metadata Variable
RAM.pal

Creat Color Palette
OTU.rarefy

Create Rarefied OTU Tables
OTU.diversity

Summarize Diversity Indices for OTU Tables
diversity.indices

Calculate True Diversity and Evenness
core.Taxa

Show Summary of Core Taxa
RAM.dates

Date Formatting for RAM
correlation

Plot Of Correlation Coefficient
RAM.rank.formatting

Taxonomic Rank Formatting
group.venn

Plot Venn Diagram For Two To Five Sets With Item Labels
location.formatting

Location Formatting
theme_ggplot

Customized Themes For GGPLOT
dissim

Calculate Dissimilarity Matrix Data
assist.NB

Negative Binomial Test For OTUID or Taxon
tax.split

Split OTU Tables By Taxonomic Rank
transpose.OTU

Take the Transpose of an OTU Table
filter.OTU

Filter OTU
group.abundance

Plot the Abundance of OTUs by Classification at a Given Taxonomic Rank
transpose.LCA

Transpose OTU Tables With LCA Annotation For Each OTU
combine.OTU

Combine Non Overlapped OTU tables From The Same Community
group.Taxa.bar

Barplot Of Taxa Distribution In Groups
get.rank

Get OTUs Classified at Taxonomic Rank(s)
col.splitup

Split Column Of Data Frame
group.heatmap

Plot OTU Abundance at a Given Rank with Metadata Annotation
core.OTU.rank

Summary Of Core OTUs
ITS1/ITS2

Sample ITS1 and ITS2 Data
group.spatial

Plot Spatial Collection Trends for Taxon Groups
assist.ado

Perform ADONIS Analysis for OTU Tables Or Taxonomic Abundance Matrix
OTU.ord

Ordination Plot For OTUs Using CCA or RDA Analysis
group.OTU

Plot Distribution of OTUs
sample.sites

Plot The Geographic Location of Samples
envis.NB

Visualize The Negative Binomial Model OF A Given Taxon OR OTUID
OTU.recap

Summarize OTU
sample.map

Plot The Geographic Location of Samples
dissim.heatmap

Plot Distance Matrix Heatmap for OTU Samples
shared.OTU

Summary of Shared OTUs Across ALL Subjects
data.subset

Subset OTU And Metadata
group.heatmap.simple

Plot a Heatmap Showing OTU Abundance by Taxonomic Classification
filter.Taxa

Filter Taxonomic Abundance Matrix by Total Counts Or Maximum Relative Abundance
match.data

Match Samples In Ecology Data Sets and Metadata
pcoa.plot

Create a PCoA plot for an OTU Table
tax.fill

Fill Missing Taxonomic Information
write.data

Write Data To CSV File
data.clust

Plot Hierarchical Cluster Of Samples Based on OTU Table or Taxonomic Abundance Matrix
sample.locations

Plot the Geographic Location of Samples
group.Taxa.box

Boxplot Of Distribution Of Taxa In Each Level of A Metadata Variable
reset.META

Reset OTU
fread.meta

Load Metadata Table
group.indicators

Plot Indicator Taxon Groups for Metadata Trends
META.clust

Plot Hierarchical Cluster Of Metadata
valid.OTU

Validate an OTU Table
valid.taxonomy

Validate And Reformat The OTU Taxonomy Column
read.meta

Open Metadata Table
group.abund.Taxa

Barplot Of Distribution Of Taxa In Groups
group.diversity

Boxplot To Compare Diversity Indices Among Groups
RAM-package

Analysis of Amplicon-Based Metagenomic Data
group.temporal

Plot Temporal Trends for Metadata and Taxon Groups
percent.classified

Calculate Percent of OTUs Classified at a Given Taxonomic Rank
dissim.plot

Plot Dissimilarity Matrix Data for Different Methods
read.OTU

Open OTU Table
data.revamp

Transform OTU Table