Getting started with phylotypr | Building the database | Classifying a single unknown sequence | Classifying multiple unknown sequences | Classifying multiple unknown sequences in parallel | Run-to-run variation | Alternative databases

Overview | Loading the example dataset | Accessing Your Data | strollur::names | strollur::count | strollur::abundance | strollur::report | strollur::summary

Saving and Loading | Export and Import | Copy

Overview | Import from mothur | Classify using phylotypr | Diversity Analysis using phyloseq | Create publication-ready plots grouped by treatment | Plot the Shannon Alpha Diversity as a boxplot: | Plot PCoA Beta Diversity: | Deep Dive

Under The Hood | Setting functions | Setting the dataset name | Setting nucleotide sequence strings | Setting sequence abundances | Merging Functions | Removing Functions | Removing Sequences | Removing Bins | Removing Samples

Creating a new dataset | Importing Data | strollur::add | Adding FASTA sequences | Adding Custom Reports | Adding Metadata | Adding Resource References | Adding Trees | strollur::assign | Assigning Abundances | Assigning Bins | Assigning Taxonomic Classifications | Assigning Bin Representatives | Assigning Treatments

Installing strollur | Importing, Accessing and Transfering Data

Using strollur::read_mothur() | Importing Individual Files | Writing mothur formatted file types

Reading Individual Files

Overview | Example

Overview | Creating strollur objects | Loading data.frames | Removing chimeras | Results

Overview | Creating strollur objects | Loading data.frames | Removing chimeras | Results

Installing rchime | Tutorials to help you get started

Process data | Import | Peak Table | Metadata | Filter | Convert retention time to "rt in minutes" or "rt in seconds" | Preprocess MS2 data | Annotating data | Molecular formula prediction | Annotations | Operational Metabolomic Units (OMUs) | Calculating distances | Clustering into OMUs | Annotation of OMUs | OMU-based Ecological Analyses | Alpha Diversity | Beta Diversity | Visualizations | Principal Coordinate Analysis (PCoA) | Hierarchical Clustering | Network Plot | Using Group Averages | Combined data frames | Heat map | Box Plot

Load required libraries | Filter MS1 feature table with mpactr | Interactive scatter plot of all input ions and their fate during filtering | Correlation between samples at different levels | Correlation between each individual sample | Correlation between technical replicates | Correlation between biological replicates | Dendrogram | Fold change analysis | Calculate fold change | Visualize fold change for compounds in a 3D scatter plot | Test for compounds with significant fold changes | Volcano plot

Load data into R | Accessing data in mpactr object | Extract peak table | Extract metadata | Reference semantics | Filtering | Mispicked ions filter | Remove ions that are above a threshold in one biological group | Remove non-reproducible ions | Remove insource fragment ions | Chaining filters together | Summary | View passing and failed ions for a single filter | View passing and failed ions for all input ions | Visualize filtering QC with tree map plot

Reference semantics | Deep copy: specifics of the R6 class

Background | Starting Up | Read count files | Read distance matrix file | Clustering the data | Selecting different clustering methods | Output data from clustering