RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

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.

AuthorWen Chen, Joshua Simpson, C. Andre Levesque
Date of publication2016-01-02 16:06:23
MaintainerWen Chen <Wen.Chen@agr.gc.ca>
LicenseMIT + file LICENSE
http://cran.r-project.org/package=RAM, https://bitbucket.org/Wen_Chen/ram_releases/src/

View on CRAN

Man pages

alignment: Sample Alignment

assist.ado: Perform ADONIS Analysis for OTU Tables Or Taxonomic Abundance...

assist.NB: Negative Binomial Test For OTUID or Taxon

assist.ordination: Perform CCA and RDA Analysis for OTU Tables

col.splitup: Split Column Of Data Frame

combine.OTU: Combine Non Overlapped OTU tables From The Same Community

core.OTU: Summary Of Core OTUs

core.OTU.rank: Summary Of Core OTUs

core.Taxa: Show Summary of Core Taxa

correlation: Plot Of Correlation Coefficient

data.clust: Plot Hierarchical Cluster Of Samples Based on OTU Table or...

data.revamp: Transform OTU Table

dissim: Calculate Dissimilarity Matrix Data

dissim.heatmap: Plot Distance Matrix Heatmap for OTU Samples

dissim.plot: Plot Dissimilarity Matrix Data for Different Methods

diversity.indices: Calculate True Diversity and Evenness

envis.NB: Visualize The Negative Binomial Model OF A Given Taxon OR...

factor.abundance: Plot the Abundance of OTUs by Classification at a Given...

filter.META: Select METADATA Variables

filter.OTU: Filter OTU

filter.Taxa: Filter Taxonomic Abundance Matrix by Total Counts Or Maximum...

fread.meta: Load Metadata Table

fread.OTU: Fast Load Large OTU Table

get.rank: Get OTUs Classified at Taxonomic Rank(s)

group.abundance: Plot the Abundance of OTUs by Classification at a Given...

group.abundance.meta: Plot the Abundance of OTUs by Classification at a Given...

group.abund.Taxa: Barplot Of Distribution Of Taxa In Groups

group.diversity: Boxplot To Compare Diversity Indices Among Groups

group.heatmap: Plot OTU Abundance at a Given Rank with Metadata Annotation

group.heatmap.simple: Plot a Heatmap Showing OTU Abundance by Taxonomic...

group.indicators: Plot Indicator Taxon Groups for Metadata Trends

group.OTU: Plot Distribution of OTUs

group.rich: Barplot Of Richness For Each Level Of A Given Metadata...

group.spatial: Plot Spatial Collection Trends for Taxon Groups

group.spec: Boxplot Of Richness For Each Level Of A Given Metadata...

group.Taxa.bar: Barplot Of Taxa Distribution In Groups

group.Taxa.box: Boxplot Of Taxa In Each Level of A Metadata Variable

group.temporal: Plot Temporal Trends for Metadata and Taxon Groups

group.venn: Plot Venn Diagram For Two To Five Sets With Item Labels

ITS1_and_ITS2: Sample ITS1 and ITS2 Data

LCA.OTU: Lowest Common Ancestor (LCA) OF EACH OTU

location.formatting: Location Formatting

match.data: Match Samples In Ecology Data Sets and Metadata

meta: Sample Metadata for ITS1/ITS2

META.clust: Plot Hierarchical Cluster Of Metadata

network_data: Creates Nodes and Edge-List For An OTU Table

OTU.diversity: Summarize Diversity Indices for OTU Tables

OTU.ord: Ordination Plot For OTUs Using CCA or RDA Analysis

OTU.rarefy: Create Rarefied OTU Tables

OTU.recap: Summarize OTU

OTU.subsets: Subset OTU And Metadata

pcoa.plot: Create a PCoA plot for an OTU Table

percent.classified: Calculate Percent of OTUs Classified at a Given Taxonomic...

phylog_taxonomy: Plot Hierarchical Taxonomic Tree

phylo_taxonomy: Plot Hierarchical Taxonomic Tree with Relative Abundance

RAM.dates: Date Formatting for RAM

RAM.factors: Factor Formatting for RAM

RAM.input.formatting: Data Input Formatting

RAM-package: Analysis of Amplicon-Based Metagenomic Data

RAM.pal: Creat Color Palette

RAM.plotting: Creating Plots with RAM

RAM.rank.formatting: Taxonomic Rank Formatting

read.meta: Open Metadata Table

read.OTU: Open OTU Table

reset.META: Reset OTU

sample.locations: Plot the Geographic Location of Samples

sample.map: Plot The Geographic Location of Samples

sample.sites: Plot The Geographic Location of Samples

seq_var: Plot Intra And Inter Specific Variation For An Alignment

shared.OTU: Summary of Shared OTUs Across ALL Subjects

shared.Taxa: Summary of Shared Taxa Across ALL Subjects

tax.abund: Aggregate OTU Data Based on Taxonomy

Taxa.ord: Ordination Plot For Taxa Groups Using CCA or RDA Analysis

tax.fill: Fill Missing Taxonomic Information

tax.split: Split OTU Tables By Taxonomic Rank

theme_ggplot: Customized Themes For GGPLOT

top.groups.plot: Plot the Top Taxon Groups

transpose.LCA: Transpose OTU Tables With LCA Annotation For Each OTU

transpose.OTU: Take the Transpose of an OTU Table

valid.OTU: Validate an OTU Table

valid.taxonomy: Validate And Reformat The OTU Taxonomy Column

write.data: Write Data To CSV File

Files in this package

RAM/R/assist.ado.R RAM/R/read_and_write_files.R RAM/R/ordination_functions.R RAM/R/network.R RAM/R/core.R RAM/R/dissim_functions_plot.R RAM/R/validation_functions.R RAM/R/taxonomy_functions.R RAM/R/plot_heatmaps.R RAM/R/theme_ggplot.R RAM/R/group.Taxa.R RAM/R/process_data.R RAM/R/seq_var.R RAM/R/metadata.R RAM/R/utility_function.R RAM/R/assist_NB.R RAM/R/internal_functions.R RAM/R/summary.R RAM/R/plot_misc.R RAM/R/group_CLUST.R RAM/R/phylo_taxonomy.R
RAM/man/OTU.rarefy.Rd RAM/man/meta.Rd RAM/man/tax.abund.Rd RAM/man/group.temporal.Rd RAM/man/valid.taxonomy.Rd RAM/man/percent.classified.Rd RAM/man/tax.fill.Rd RAM/man/RAM.rank.formatting.Rd RAM/man/theme_ggplot.Rd RAM/man/Taxa.ord.Rd RAM/man/group.Taxa.bar.Rd RAM/man/alignment.Rd RAM/man/META.clust.Rd RAM/man/dissim.plot.Rd RAM/man/OTU.diversity.Rd RAM/man/fread.meta.Rd RAM/man/shared.OTU.Rd RAM/man/core.Taxa.Rd RAM/man/network_data.Rd RAM/man/location.formatting.Rd RAM/man/assist.NB.Rd RAM/man/sample.map.Rd RAM/man/group.venn.Rd RAM/man/correlation.Rd RAM/man/assist.ado.Rd RAM/man/dissim.heatmap.Rd RAM/man/group.abund.Taxa.Rd RAM/man/transpose.OTU.Rd RAM/man/seq_var.Rd RAM/man/get.rank.Rd RAM/man/LCA.OTU.Rd RAM/man/read.meta.Rd RAM/man/RAM.factors.Rd RAM/man/RAM.pal.Rd RAM/man/phylo_taxonomy.Rd RAM/man/ITS1_and_ITS2.Rd RAM/man/read.OTU.Rd RAM/man/RAM.plotting.Rd RAM/man/RAM-package.Rd RAM/man/core.OTU.Rd RAM/man/group.abundance.meta.Rd RAM/man/diversity.indices.Rd RAM/man/sample.sites.Rd RAM/man/filter.META.Rd RAM/man/assist.ordination.Rd RAM/man/group.diversity.Rd RAM/man/dissim.Rd RAM/man/group.heatmap.Rd RAM/man/OTU.recap.Rd RAM/man/RAM.input.formatting.Rd RAM/man/combine.OTU.Rd RAM/man/group.indicators.Rd RAM/man/sample.locations.Rd RAM/man/match.data.Rd RAM/man/group.heatmap.simple.Rd RAM/man/OTU.ord.Rd RAM/man/group.abundance.Rd RAM/man/data.clust.Rd RAM/man/RAM.dates.Rd RAM/man/core.OTU.rank.Rd RAM/man/group.spatial.Rd RAM/man/write.data.Rd RAM/man/fread.OTU.Rd RAM/man/group.spec.Rd RAM/man/filter.OTU.Rd RAM/man/col.splitup.Rd RAM/man/transpose.LCA.Rd RAM/man/group.OTU.Rd RAM/man/filter.Taxa.Rd RAM/man/shared.Taxa.Rd RAM/man/OTU.subsets.Rd RAM/man/group.Taxa.box.Rd RAM/man/phylog_taxonomy.Rd RAM/man/valid.OTU.Rd RAM/man/pcoa.plot.Rd RAM/man/envis.NB.Rd RAM/man/data.revamp.Rd RAM/man/factor.abundance.Rd RAM/man/top.groups.plot.Rd RAM/man/reset.META.Rd RAM/man/group.rich.Rd RAM/man/tax.split.Rd

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