Man pages for Gibbons-Lab/mbtools
Provides helper functions for microbiome preprocessing and analysis
| align_long_reads | Align long reads (for instance from nanopore sequencing) to a... |
| align_short_reads | Aligns metagenomic shotgun reads against a reference. |
| annotate_contigs | Annotate diamond database hits with transcript info. |
| annotate_silva | Annotate the sequences in the SILVA database file. |
| as.matrix.mbquant | Convert a mbquant data table to a matrix. |
| as_phyloseq | Converts the denoise artifact to a phyloseq object. |
| association | Run differential association tests between taxa counts and... |
| bin_coverage | Reads the coverage from a set of alignments and calculates... |
| bracken_to_phyloseq | Converts BRACKEN results to a phyloseq object. |
| build_lineage | Build the lineage from a SILVA path string. |
| combinatorial_association | Run differential association tests between between all... |
| config_align | Build a configuration for the alignment workflows. |
| config_association | Build a configuration for the alignment workflows. |
| config_chimera | Build a configuration for chimera removal. |
| config_count | Build a configuration for the transcript counting workflow. |
| config_coverage | Build a configuration for the coverage workflow. |
| config_demultiplex | Build a configuration for the demultiplexing workflow. |
| config_denoise | Build a configuration for the DADA2 workflow. |
| config_layout | Build a configuration for the plate layout. |
| config_power | Build a configuration for power analysis. |
| config_preprocess | Build a configuration for raw read preprocessing. |
| config_reference | Build a configuration for the reference removal workflow. |
| config_rep | Build a configuration for the rate workflow. |
| config_slimm | Build a configuration for the SLIMM workflow. |
| config_sra | Build a configuration for the SRA submission workflow. |
| count_references | Count alignment hits to a reference database. |
| demultiplex | Splits FASTQ files into individual samples. |
| denoise | Runs a full DADA2 workflow. |
| discretize | Discretize all continuous variables in a data frame. |
| download_bacterial_transcripts | Download the entire ENSEMBL transcript DB for bacteria. |
| download_files | Download a list of files. |
| download_sra | Download data from SRA. |
| effective_lengths | Calculate the effective transcript lengths. This is the mean... |
| em_count | Count transcripts using an Expectation Maximization (EM)... |
| ERR260132 | Precomputed lineage calling and coverage example. |
| filter_counts | Filter low presence taxa from a count matrix. |
| filter_reference | Filter a set of reference sequences from the data set.seed |
| find_read_files | Find read files in a given directory. |
| find_taxa | Checks whether taxa from one taxonomy table are contained in... |
| layout | Generate a plate layout from a sample manifest. |
| mbtools | mbtools. |
| merge_transcripts | Merge transcripts into a single database |
| mock_plot | Creates a plot of measured taxa quantifications vs. reference... |
| mockrobiota | Downloads a complete data set from mockrobiota. |
| mothur_to_dada | Converts taxa annotations from mothur format to dada2 format. |
| normalize | Normalize a set of read counts across samples |
| orlitsky | Orlitsky's diminishing attenuation estimator (q2/3). |
| parse_ensembl_id | Parse annotations from an ENSEMBL id |
| plot_bb_fits | Plot the Betabinomial fits for all taxa in a phyloseq object |
| plot_counts | Plots counts for several taxa across a co-variable |
| plot_entropy | Plots the distribution of base entropy for each cycle. |
| plot_lengths | Plots the distribution of sequence lengths with acceptable... |
| plot_qualities | Plots the quality profile for an entire experiment. |
| plot_taxa | Plots relative distribution for taxa across samples. |
| power_analysis | Run a power analysis for microbe abundances from a reference... |
| preprocess | Runs preprocessing of sequencing reads. |
| quality_control | Workflow for basic quality assessment of the read files. |
| quality_profile | Get the quality profiles and base calls for each cycle across... |
| read_bam | Read alignments from a BAM file. |
| read_blast | Read a blast hit/alignment file. |
| read_length | Heuristic to get the median read length from a BAM... |
| read_slimm | Reads SLIMM output to a data table. |
| read_slimm_coverage | Reads SLIMM coverage to a data table. |
| reads_to_phyloseq | Converts read count data to a phyloseq object. |
| remove_chimeras | Removes chimeric reads from amplicon sequencing data. |
| remove_reference | Removes sequence that map to a given reference. |
| replication_rates | Estimate replication rates by the iRep method. |
| select | Very simple select for mbtools artifacts. Just gets a... |
| silva_build_taxonomy | Build the lineages for the entire SILVA database. |
| slimm | Quantifies abundances and coverage using SLIMM. |
| slimm_files | The SLIMM taxonomy databases |
| sra_submission | Prepare submission files for the NCBI sequence read archive... |
| standardize | Standardize all continuous columns of a data frame. |
| taxa_count | Counts the reads for a specific taxonomy level. |
| taxa_metrics | Calculates what percentage of taxa was found in a reference... |
| taxa_quants | Compares taxa quantification from a measurement to a... |
| types | Applies the specified types to a data frame-like object. |
| with_classification | Quantify classification rates for each taxonomic rank. |
