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.

Install the latest version of this package by entering the following in R:
install.packages("RAM")
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
Version1.2.1.3
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

Functions

alignment Man page
assist.ado Man page
assist.cca Man page
assist.NB Man page
assist.ordination Man page
assist.rda Man page
col.splitup Man page
combine.OTU Man page
core.OTU Man page
core.OTU.rank Man page
core.Taxa Man page
correlation Man page
data.clust Man page
data.revamp Man page
data.subset Man page
dissim Man page
dissim.alleig.plot Man page
dissim.clust Man page
dissim.clust.plot Man page
dissim.eig Man page
dissim.eig.plot Man page
dissim.GOF Man page
dissim.GOF.plot Man page
dissim.heatmap Man page
dissim.ord Man page
dissim.ord.plot Man page
dissim.plot Man page
dissim.pvar Man page
dissim.pvar.plot Man page
dissim.tree Man page
dissim.tree.plot Man page
diversity.indices Man page
envis.NB Man page
evenness Man page
factor.abundance Man page
filter.META Man page
filter.OTU Man page
filter.Taxa Man page
fread.meta Man page
fread.OTU Man page
get.rank Man page
group.abundance Man page
group.abundance.meta Man page
group.abund.Taxa Man page
group.diversity Man page
group.heatmap Man page
group.heatmap.simple Man page
group.indicators Man page
group.OTU Man page
group.rich Man page
group.spatial Man page
group.spec Man page
group.Taxa.bar Man page
group.Taxa.box Man page
group.temporal Man page
group.top.number Man page
group.top.percent Man page
group.venn Man page
ITS1 Man page
ITS1/ITS2 Man page
ITS2 Man page
LCA.OTU Man page
location.formatting Man page
match.data Man page
meta Man page
META.clust Man page
network_data Man page
OTU.cca Man page
OTU.diversity Man page
OTU.ord Man page
OTU.rarefy Man page
OTU.rda Man page
OTU.recap Man page
pcoa.plot Man page
percent.classified Man page
phylog_taxonomy Man page
phylo_taxonomy Man page
RAM Man page
RAM.border Man page
RAM.color Man page
RAM.dates Man page
RAM.factors Man page
RAM.input.formatting Man page
RAM-package Man page
RAM.pal Man page
RAM.plotting Man page
RAM.rank.formatting Man page
read.meta Man page
read.OTU Man page
reformat.taxonomy Man page
reset.META Man page
sample.locations Man page
sample.map Man page
sample.sites Man page
seq_var Man page
shared.OTU Man page
shared.Taxa Man page
tax.abund Man page
Taxa.cca Man page
Taxa.ord Man page
Taxa.rda Man page
tax.fill Man page
tax.split Man page
top.groups.plot Man page
transpose.LCA Man page
transpose.OTU Man page
true.diversity Man page
valid.OTU Man page
valid.taxonomy Man page
write.data Man page

Files

inst
inst/CITATION
inst/extdata
inst/extdata/map.fortify.list.RData
NAMESPACE
NEWS
data
data/ITS2.RData
data/ITS1.RData
data/alignment.RData
data/meta.RData
R
R/assist.ado.R R/read_and_write_files.R R/ordination_functions.R R/network.R R/core.R R/dissim_functions_plot.R R/validation_functions.R R/taxonomy_functions.R R/plot_heatmaps.R R/theme_ggplot.R R/group.Taxa.R R/process_data.R R/seq_var.R R/metadata.R R/utility_function.R R/assist_NB.R R/internal_functions.R R/summary.R R/plot_misc.R R/group_CLUST.R R/phylo_taxonomy.R
MD5
build
build/RAM.pdf
DESCRIPTION
ChangeLog
man
man/OTU.rarefy.Rd man/meta.Rd man/tax.abund.Rd man/group.temporal.Rd man/valid.taxonomy.Rd man/percent.classified.Rd man/tax.fill.Rd man/RAM.rank.formatting.Rd man/theme_ggplot.Rd man/Taxa.ord.Rd man/group.Taxa.bar.Rd man/alignment.Rd man/META.clust.Rd man/dissim.plot.Rd man/OTU.diversity.Rd man/fread.meta.Rd man/shared.OTU.Rd man/core.Taxa.Rd man/network_data.Rd man/location.formatting.Rd man/assist.NB.Rd man/sample.map.Rd man/group.venn.Rd man/correlation.Rd man/assist.ado.Rd man/dissim.heatmap.Rd man/group.abund.Taxa.Rd man/transpose.OTU.Rd man/seq_var.Rd man/get.rank.Rd man/LCA.OTU.Rd man/read.meta.Rd man/RAM.factors.Rd man/RAM.pal.Rd man/phylo_taxonomy.Rd man/ITS1_and_ITS2.Rd man/read.OTU.Rd man/RAM.plotting.Rd man/RAM-package.Rd man/core.OTU.Rd man/group.abundance.meta.Rd man/diversity.indices.Rd man/sample.sites.Rd man/filter.META.Rd man/assist.ordination.Rd man/group.diversity.Rd man/dissim.Rd man/group.heatmap.Rd man/OTU.recap.Rd man/RAM.input.formatting.Rd man/combine.OTU.Rd man/group.indicators.Rd man/sample.locations.Rd man/match.data.Rd man/group.heatmap.simple.Rd man/OTU.ord.Rd man/group.abundance.Rd man/data.clust.Rd man/RAM.dates.Rd man/core.OTU.rank.Rd man/group.spatial.Rd man/write.data.Rd man/fread.OTU.Rd man/group.spec.Rd man/filter.OTU.Rd man/col.splitup.Rd man/transpose.LCA.Rd man/group.OTU.Rd man/filter.Taxa.Rd man/shared.Taxa.Rd man/OTU.subsets.Rd man/group.Taxa.box.Rd man/phylog_taxonomy.Rd man/valid.OTU.Rd man/pcoa.plot.Rd man/envis.NB.Rd man/data.revamp.Rd man/factor.abundance.Rd man/top.groups.plot.Rd man/reset.META.Rd man/group.rich.Rd man/tax.split.Rd
LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.