Miscellaneous Functions for Metabarcoding Analysis
Plot accumulation curves with balanced modality and depth rarefaction
Plot accumulation curves for phyloseq-class object
Compute the number of sequence to obtain a given proportion of ASV in ...
Add information from blast_pq() to the tax_table slot of a **phylo...
Add dna in refseq slot of a physeq object using taxa names and ren...
Add information about Guild for FUNGI the FUNGuild databse
Add information to sample_data slot of a phyloseq-class object
Add new taxonomic rank to a phyloseq object.
Permanova on a phyloseq object
Permanova (adonis) on permutations of rarefaction even depth
List the size of all objects of the GlobalEnv.
Run ANCOMBC2 on phyloseq object
Test if the mean number of sequences by samples is link to the modalit...
Transform the otu_table of a phyloseq-class object into a `phyloseq-...
Assign taxonomy using blastn algorithm and the blast software
Assign taxonomy with dada2 using 2 steps assignTaxonomy and assignSpec...
A wrapper of IdTaxa
Assign Taxonomy using Sintax algorithm of Vsearch
Assign taxonomy using LCA
Visualization of two samples for comparison
Blast all sequence of refseq slot of a phyloseq-classobject agains...
Blast some sequence against sequences from of a derep-classobject.
Blast some sequence against refseq slot of a phyloseq-classobject.
Build phylogenetic trees from refseq slot of a phyloseq object
Detect for chimera taxa using [vsearch](https://github.com/torognes/vs...
Search for a list of sequence in an object to remove chimera taxa usin...
Plot OTU circle for phyloseq-class object
Clean phyloseq object by removing empty samples and taxa
Compare samples in pairs using diversity and number of ASV including s...
Count sequences in fasta or fastq file
Remove primers using cutadapt
Compute different functions for different class of vector.
Compute paired distances among matrix (e.g. otu_table)
Calculate ecological distance among positive controls vs distance for ...
Distribution of sequences across a factor for one taxon
Translates a factor into colors.
Filter taxa of a phyloseq object based on the minimum number of sequen...
Filter taxa by cleaning taxa with NA at given taxonomic rank(s)
Filter undesirable taxa using blast against a custom database.
A wrapper of the function dada2::filterAndTrim() to use in [targets]...
Format a fasta database in dada2 format for Species assignment
Format a fasta database in dada2 format
Format a fasta database in sintax format
Create a visualization table to describe taxa distribution across a mo...
Assign Guilds to Organisms Based on Taxonomic Classification
Funky palette color
Get the extension of a file
Retrieve the FUNGuild database
Alluvial plot for taxonomy and samples factor vizualisation
Box/Violin plots for between-subjects comparisons of Hill Number
Scatterplot with marginal distributions and statistical results agains...
Venn diagram of phyloseq-class object using `ggVennDiagram::ggVennDi...
Automated model selection and multimodel inference with (G)LMs for phy...
Performs graph-based permutation tests on phyloseq object
Hill Diversities and Corresponding Accumulation Curves for phyloseq
Graphical representation of hill number 0, 1 and 2 across a factor
Test multiple times effect of factor on Hill diversity with different ...
Calculate hill number and compute Tuckey post-hoc test
iNterpolation and EXTrapolation of Hill numbers (with iNEXT)
Test if cutadapt is installed.
Test if falco is installed.
Test if krona is installed.
Test if mumu is installed.
Test if swarm is installed.
Test if vsearch is installed.
Make Krona files using [KronaTools](https://github.com/marbl/Krona/wik...
Compute and test local contributions to beta diversity (LCBD) of sampl...
A wrapper of DECIPHER::LearnTaxa()
List fastq files
Lulu reclustering of class physeq
Post Clustering Curation of Amplicon Data.
Merge Krona files using [KronaTools](https://github.com/marbl/Krona/wi...
Merge samples by a sample variable or factor
Merge taxa in groups (vectorized version)
Deprecated function(s) in the MiscMetabar package
MiscMetabar package
Visualization of a collection of couples of samples for comparison
Test and plot multipatt result
Multiple plot function
Plot taxonomic distribution across 3 taxonomic levels and optionally o...
MUMU reclustering of class physeq
Discard legend in ggplot2
Normalize OTU table using samples depth
Convert a value (or a fraction x/y) in percentage
Convert phyloseq OTU count data into DGEList for edgeR package
Return a DNAStringSet object from either a character vector of DNA seq...
Plot ANCOMBC2 result for phyloseq object
Plot kmer complexity of references sequences of a phyloseq object
Plot DESeq2 results for a phyloseq or a DESeq2 object.
Plot edgeR results for a phyloseq or a edgeR object.
Plot information about Guild from tax_table slot previously created wi...
Plot and test local contributions to beta diversity (LCBD) of samples
Plot the result of a mt test phyloseq::mt()
Plot the nucleotide proportion at both extremity of the sequences
Plot the nucleotide proportion of references sequences
Plot species contributions to beta diversity (SCBD) of samples
A diagnostic plot of the number of sequences per samples
Plot taxonomic distribution in function of a factor with stacked bar i...
Plot a tsne low dimensional representation of a phyloseq object
Plot the partition the variation of a phyloseq object
Recluster sequences of an object of class physeqor a list of DNA seq...
Build a sample information tibble from physeq object
Rarefy (equalize) the number of samples per modality of a factor
Read phyloseq object from multiple csv tables and a phylogenetic tree ...
Rename samples of an otu_table
Rename the samples of a phyloseq slot
Reorder taxa in otu_table/tax_table/refseq slot of a phyloseq object
Resolve conflict in a vector of taxonomy values
Ridge plot of a phyloseq object
rotl wrapper for phyloseq data
Match sample names from sam_data and fastq files
Load sample data from file and rename samples using names of samples a...
Sankey plot of phyloseq-class object
A wrapper of write_pq to save in all three possible formats
Search for exact matching of sequences
Select one sample from a physeq object
Select a subset of taxa in a specified order where possible
Filter ancombc_pq results
Simplify taxonomy by removing some unused characters such as "k__"
Scaling with ranked subsampling (SRS) curve of phyloseq object
Subsample a fastq file copying the n_seq first sequences in a given fo...
Subset samples using a conditional boolean vector.
Subset taxa using a conditional named boolean vector.
Subset taxa using a taxa control or distribution based method
Summarize a phyloseq-class object using a plot.
Re-cluster sequences of an object of class physeqor cluster a list o...
Plot the distribution of sequences or ASV in one taxonomic levels
Make a datatable with the taxonomy of a phyloseq-class object
Force taxa to be in columns in the otu_table of a physeq object
Force taxa to be in columns in the otu_table of a physeq object
Show taxa which are present in only one given level of a modality
Summarize information from sample data in a table
Summarize a tax_table (taxonomic slot of phyloseq object) using gtsumm...
Track the number of reads (= sequences), samples and cluster (e.g. ASV...
Track the number of reads (= sequences), samples and cluster (e.g. ASV...
Adds transparency to a vector of colors
Plot treemap of 2 taxonomic levels
Compute tSNE position of samples from a phyloseq object
Computes a manifold approximation and projection (UMAP) for phyloseq o...
Get the unique value in x or NA if none
Make upset plot for phyloseq object.
Test for differences between intersections
Partition the Variation of a phyloseq object by 2, 3, or 4 Explanatory...
Partition the Variation of a phyloseq object with rarefaction permutat...
Venn diagram of phyloseq-class object
Verify the validity of a phyloseq object
Search for a list of sequence in a fasta file against physeq reference...
Recluster sequences of an object of class physeqor cluster a list of...
Save phyloseq object in the form of multiple csv tables.
Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
Useful links