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RAM (version 1.2.1.3)

R for Amplicon-Sequencing-Based Microbial-Ecology

Description

Characterizing environmental microbiota diversity using amplicon-based next generation sequencing (NGS) data. Functions are developed to manipulate operational taxonomic unit (OTU) table, perform descriptive and inferential statistics, and generate publication-quality plots.

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Version

Install

install.packages('RAM')

Monthly Downloads

57

Version

1.2.1.3

License

MIT + file LICENSE

Maintainer

Wen Chen

Last Published

January 2nd, 2016

Functions in RAM (1.2.1.3)

match.data

Match Samples In Ecology Data Sets and Metadata
group.heatmap

Plot OTU Abundance at a Given Rank with Metadata Annotation
RAM.dates

Date Formatting for RAM
diversity.indices

Calculate True Diversity and Evenness
network_data

Creates Nodes and Edge-List For An OTU Table
phylo_taxonomy

Plot Hierarchical Taxonomic Tree with Relative Abundance
transpose.LCA

Transpose OTU Tables With LCA Annotation For Each OTU
top.groups.plot

Plot the Top Taxon Groups
Taxa.ord

Ordination Plot For Taxa Groups Using CCA or RDA Analysis
correlation

Plot Of Correlation Coefficient
RAM.plotting

Creating Plots with RAM
RAM-package

Analysis of Amplicon-Based Metagenomic Data
fread.meta

Load Metadata Table
filter.Taxa

Filter Taxonomic Abundance Matrix by Total Counts Or Maximum Relative Abundance
LCA.OTU

Lowest Common Ancestor (LCA) OF EACH OTU
RAM.factors

Factor Formatting for RAM
assist.NB

Negative Binomial Test For OTUID or Taxon
data.revamp

Transform OTU Table
data.clust

Plot Hierarchical Cluster Of Samples Based on OTU Table or Taxonomic Abundance Matrix
shared.Taxa

Summary of Shared Taxa Across ALL Subjects
group.abund.Taxa

Barplot Of Distribution Of Taxa In Groups
group.spatial

Plot Spatial Collection Trends for Taxon Groups
data.subset

Subset OTU And Metadata
dissim

Calculate Dissimilarity Matrix Data
shared.OTU

Summary of Shared OTUs Across ALL Subjects
tax.fill

Fill Missing Taxonomic Information
factor.abundance

Plot the Abundance of OTUs by Classification at a Given Taxonomic Rank For Each Level of A Metadata Category Variable.
group.spec

Boxplot Of Richness For Each Level Of A Given Metadata Variable
location.formatting

Location Formatting
percent.classified

Calculate Percent of OTUs Classified at a Given Taxonomic Rank
OTU.ord

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

Summarize OTU
dissim.plot

Plot Dissimilarity Matrix Data for Different Methods
filter.META

Select METADATA Variables
group.abundance.meta

Plot the Abundance of OTUs by Classification at a Given Taxonomic Rank
read.meta

Open Metadata Table
ITS1/ITS2

Sample ITS1 and ITS2 Data
sample.sites

Plot The Geographic Location of Samples
OTU.diversity

Summarize Diversity Indices for OTU Tables
group.rich

Barplot Of Richness For Each Level Of A Given Metadata Variable
valid.OTU

Validate an OTU Table
seq_var

Plot Intra And Inter Specific Variation For An Alignment
get.rank

Get OTUs Classified at Taxonomic Rank(s)
core.Taxa

Show Summary of Core Taxa
alignment

Sample Alignment
RAM.input.formatting

Data Input Formatting
RAM.rank.formatting

Taxonomic Rank Formatting
col.splitup

Split Column Of Data Frame
group.indicators

Plot Indicator Taxon Groups for Metadata Trends
sample.locations

Plot the Geographic Location of Samples
phylog_taxonomy

Plot Hierarchical Taxonomic Tree
reset.META

Reset OTU
group.heatmap.simple

Plot a Heatmap Showing OTU Abundance by Taxonomic Classification
group.venn

Plot Venn Diagram For Two To Five Sets With Item Labels
meta

Sample Metadata for ITS1/ITS2
assist.ordination

Perform CCA and RDA Analysis for OTU Tables
pcoa.plot

Create a PCoA plot for an OTU Table
group.OTU

Plot Distribution of OTUs
tax.split

Split OTU Tables By Taxonomic Rank
core.OTU

Summary Of Core OTUs
write.data

Write Data To CSV File
tax.abund

Aggregate OTU Data Based on Taxonomy
OTU.rarefy

Create Rarefied OTU Tables
read.OTU

Open OTU Table
combine.OTU

Combine Non Overlapped OTU tables From The Same Community
fread.OTU

Fast Load Large OTU Table
dissim.heatmap

Plot Distance Matrix Heatmap for OTU Samples
transpose.OTU

Take the Transpose of an OTU Table
envis.NB

Visualize The Negative Binomial Model OF A Given Taxon OR OTUID
RAM.pal

Creat Color Palette
group.abundance

Plot the Abundance of OTUs by Classification at a Given Taxonomic Rank
valid.taxonomy

Validate And Reformat The OTU Taxonomy Column
group.Taxa.bar

Barplot Of Taxa Distribution In Groups
group.temporal

Plot Temporal Trends for Metadata and Taxon Groups
filter.OTU

Filter OTU
group.diversity

Boxplot To Compare Diversity Indices Among Groups
sample.map

Plot The Geographic Location of Samples
META.clust

Plot Hierarchical Cluster Of Metadata
core.OTU.rank

Summary Of Core OTUs
group.Taxa.box

Boxplot Of Taxa In Each Level of A Metadata Variable
assist.ado

Perform ADONIS Analysis for OTU Tables Or Taxonomic Abundance Matrix
theme_ggplot

Customized Themes For GGPLOT