Documentation

Functions in Bioinformatics Toolbox

  • By Category | Alphabetical List
  • High-Throughput Sequencing

    Data Import and Management

    fastainfo Return information about FASTA file
    fastaread Read data from FASTA file
    fastawrite Write to file using FASTA format
    fastqinfo Return information about FASTQ file
    fastqread Read data from FASTQ file
    fastqwrite Write to file using FASTQ format
    saminfo Return information about Sequence Alignment/Map (SAM) file
    samread Read data from Sequence Alignment/Map (SAM) file
    baminfo Return information about Binary Sequence Alignment/Map (BAM) file
    bamread Read data from Binary Sequence Alignment/Map (BAM) file
    bamindexread Read Binary Sequence Alignment/Map Index (BAI) file
    goannotread Read annotations from Gene Ontology annotated file
    soapread Read data from Short Oligonucleotide Analysis Package (SOAP) file
    BioIndexedFile Allow quick and efficient access to large text file with nonuniform-size entries
    BioMap Contain sequence, quality, alignment, and mapping data
    BioRead Contain sequence and quality data
    BioReadQualityStatistics Quality statistics from a short-read sequence file
    GFFAnnotation Represent General Feature Format (GFF) annotations
    GTFAnnotation Represent Gene Transfer Format (GTF) annotations

    Preprocessing

    BioMap Contain sequence, quality, alignment, and mapping data
    BioReadQualityStatistics Quality statistics from a short-read sequence file
    GFFAnnotation Represent General Feature Format (GFF) annotations
    GTFAnnotation Represent Gene Transfer Format (GTF) annotations

    RNA

    ngsbrowser Open NGS Browser to visualize and explore short-read sequence alignments
    align2cigar Convert aligned sequences to corresponding Compact Idiosyncratic Gapped Alignment Report (CIGAR) format strings
    cigar2align Convert unaligned sequences to aligned sequences using Compact Idiosyncratic Gapped Alignment Report (CIGAR) format strings
    bowtie Map short reads to reference sequence using Burrows-Wheeler transform
    bowtiebuild Generate index using Burrows-Wheeler transform
    mattest Perform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
    mafdr Estimate false discovery rate (FDR) for multiple hypothesis testing
    mavolcanoplot Create significance versus gene expression ratio (fold change) scatter plot of microarray data
    mairplot Create intensity versus ratio scatter plot of microarray data
    maboxplot Create box plot for microarray data
    nbintest Unpaired hypothesis test for short-read count data with small sample sizes
    clustergram Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
    redbluecmap Create red and blue colormap
    redgreencmap Create red and green colormap
    metafeatures Attractor metagene algorithm for feature engineering using mutual information-based learning
    rankfeatures Rank key features by class separability criteria
    randfeatures Generate randomized subset of features
    fitcknn Fit k-nearest neighbor classifier
    knnimpute Impute missing data using nearest-neighbor method
    classperf Evaluate performance of classifier
    crossvalind Generate cross-validation indices
    BioRead Contain sequence and quality data
    BioMap Contain sequence, quality, alignment, and mapping data
    BioReadQualityStatistics Quality statistics from a short-read sequence file
    GFFAnnotation Represent General Feature Format (GFF) annotations
    GTFAnnotation Represent Gene Transfer Format (GTF) annotations
    NegativeBinomialTest Unpaired hypothesis test result
    HeatMap Display heat map of matrix data and create HeatMap object
    HeatMap object Object containing matrix and heat map display properties
    clustergram Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
    clustergram object Object containing hierarchical clustering analysis data
    DataMatrix Create DataMatrix object
    DataMatrix object Data structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers

    DNA

    ngsbrowser Open NGS Browser to visualize and explore short-read sequence alignments
    mafdr Estimate false discovery rate (FDR) for multiple hypothesis testing
    mle Maximum likelihood estimates
    nbinpdf Negative binomial probability density function
    chromosomeplot Plot chromosome ideogram with G-banding pattern
    cpgisland Locate CpG islands in DNA sequence
    mspeaks Convert raw peak data to peak list (centroided data)
    align2cigar Convert aligned sequences to corresponding Compact Idiosyncratic Gapped Alignment Report (CIGAR) format strings
    cigar2align Convert unaligned sequences to aligned sequences using Compact Idiosyncratic Gapped Alignment Report (CIGAR) format strings
    bowtie Map short reads to reference sequence using Burrows-Wheeler transform
    bowtiebuild Generate index using Burrows-Wheeler transform
    BioRead Contain sequence and quality data
    BioMap Contain sequence, quality, alignment, and mapping data
    BioReadQualityStatistics Quality statistics from a short-read sequence file
    GFFAnnotation Represent General Feature Format (GFF) annotations
    GTFAnnotation Represent Gene Transfer Format (GTF) annotations

    Gene Ontology

    goannotread Read annotations from Gene Ontology annotated file
    num2goid Convert numbers to Gene Ontology IDs
    geneont Data structure containing Gene Ontology (GO) information

    Network Analysis and Visualization

    graphallshortestpaths Find all shortest paths in graph
    graphconncomp Find strongly or weakly connected components in graph
    graphisdag Test for cycles in directed graph
    graphisomorphism Find isomorphism between two graphs
    graphisspantree Determine if tree is spanning tree
    graphmaxflow Calculate maximum flow in directed graph
    graphminspantree Find minimal spanning tree in graph
    graphpred2path Convert predecessor indices to paths
    graphshortestpath Solve shortest path problem in graph
    graphtopoorder Perform topological sort of directed acyclic graph
    graphtraverse Traverse graph by following adjacent nodes
    biograph Create biograph object
    biograph object Data structure containing generic interconnected data used to implement directed graph

    Microarray Analysis

    Data Import and Management

    affyread Read microarray data from Affymetrix GeneChip file
    affysnpannotread Read Affymetrix Mapping DNA array data from CSV-format annotation file
    affyprobeseqread Read data file containing probe sequence information for Affymetrix GeneChip array
    celintensityread Read probe intensities from Affymetrix CEL files
    getgeodata Retrieve Gene Expression Omnibus (GEO) format data
    geoseriesread Read Gene Expression Omnibus (GEO) Series (GSE) format data
    geosoftread Read Gene Expression Omnibus (GEO) SOFT format data
    galread Read microarray data from GenePix array list file
    gprread Read microarray data from GenePix Results (GPR) file
    agferead Read Agilent Feature Extraction Software file
    ilmnbsread Read gene expression data exported from Illumina BeadStudio software
    imageneread Read microarray data from ImaGene Results file
    sptread Read data from SPOT file
    goannotread Read annotations from Gene Ontology annotated file
    cytobandread Read cytogenetic banding information
    bioma.ExpressionSet Contain data from microarray gene expression experiment
    bioma.data.ExptData Contain data values from microarray experiment
    bioma.data.MetaData Contain metadata from microarray experiment
    bioma.data.MIAME Contain experiment information from microarray gene expression experiment

    Preprocessing

    affyrma Perform Robust Multi-array Average (RMA) procedure on Affymetrix microarray probe-level data
    affygcrma Perform GC Robust Multi-array Average (GCRMA) procedure on Affymetrix microarray probe-level data
    affyinvarsetnorm Perform rank invariant set normalization on probe intensities from multiple Affymetrix CEL or DAT files
    affyprobeaffinities Compute Affymetrix probe affinities from their sequences and MM probe intensities
    affysnpintensitysplit Split Affymetrix SNP probe intensity information for alleles A and B
    affysnpquartets Create table of SNP probe quartet results for Affymetrix probe set
    probesetvalues Create table of Affymetrix probe set intensity values
    probesetlookup Look up information for Affymetrix probe set
    probesetplot Plot Affymetrix probe set intensity values
    probesetlink Display probe set information on NetAffx Web site
    probelibraryinfo Create table of probe set library information
    rmabackadj Perform background adjustment on Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure
    rmasummary Calculate gene expression values from Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure
    gcrma Perform GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization on Affymetrix microarray probe-level data
    gcrmabackadj Perform GC Robust Multi-array Average (GCRMA) background adjustment on Affymetrix microarray probe-level data using sequence information
    zonebackadj Perform background adjustment on Affymetrix microarray probe-level data using zone-based method
    manorm Normalize microarray data
    quantilenorm Quantile normalization over multiple arrays
    mainvarsetnorm Perform rank invariant set normalization on gene expression values from two experimental conditions or phenotypes
    malowess Smooth microarray data using Lowess method
    exprprofrange Calculate range of gene expression profiles
    exprprofvar Calculate variance of gene expression profiles
    geneentropyfilter Remove genes with low entropy expression values
    genelowvalfilter Remove gene profiles with low absolute values
    generangefilter Remove gene profiles with small profile ranges
    genevarfilter Filter genes with small profile variance
    maimage Spatial image for microarray data
    microplateplot Display visualization of microtiter plate
    ilmnbslookup Look up Illumina BeadStudio target (probe) sequence and annotation information
    magetfield Extract data from microarray structure

    Expression Analysis

    mattest Perform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
    mafdr Estimate false discovery rate (FDR) for multiple hypothesis testing
    mavolcanoplot Create significance versus gene expression ratio (fold change) scatter plot of microarray data
    mairplot Create intensity versus ratio scatter plot of microarray data
    maboxplot Create box plot for microarray data
    maloglog Create loglog plot of microarray data
    mapcaplot Create Principal Component Analysis (PCA) plot of microarray data
    nbintest Unpaired hypothesis test for short-read count data with small sample sizes
    clustergram Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
    redbluecmap Create red and blue colormap
    redgreencmap Create red and green colormap
    probesetplot Plot Affymetrix probe set intensity values
    metafeatures Attractor metagene algorithm for feature engineering using mutual information-based learning
    rankfeatures Rank key features by class separability criteria
    randfeatures Generate randomized subset of features
    fitcknn Fit k-nearest neighbor classifier
    knnimpute Impute missing data using nearest-neighbor method
    classperf Evaluate performance of classifier
    crossvalind Generate cross-validation indices
    DataMatrix Create DataMatrix object
    DataMatrix object Data structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
    bioma.ExpressionSet Contain data from microarray gene expression experiment
    bioma.data.ExptData Contain data values from microarray experiment
    bioma.data.MetaData Contain metadata from microarray experiment
    bioma.data.MIAME Contain experiment information from microarray gene expression experiment
    NegativeBinomialTest Unpaired hypothesis test result
    HeatMap Display heat map of matrix data and create HeatMap object
    HeatMap object Object containing matrix and heat map display properties
    clustergram Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
    clustergram object Object containing hierarchical clustering analysis data

    Genetic Variant Analysis

    cghcbs Perform circular binary segmentation (CBS) on array-based comparative genomic hybridization (aCGH) data
    cghfreqplot Display frequency of DNA copy number alterations across multiple samples
    chromosomeplot Plot chromosome ideogram with G-banding pattern
    gcrma Perform GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization on Affymetrix microarray probe-level data
    gcrmabackadj Perform GC Robust Multi-array Average (GCRMA) background adjustment on Affymetrix microarray probe-level data using sequence information
    mattest Perform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
    mafdr Estimate false discovery rate (FDR) for multiple hypothesis testing
    mavolcanoplot Create significance versus gene expression ratio (fold change) scatter plot of microarray data
    mairplot Create intensity versus ratio scatter plot of microarray data
    maboxplot Create box plot for microarray data
    maloglog Create loglog plot of microarray data
    mapcaplot Create Principal Component Analysis (PCA) plot of microarray data
    nbintest Unpaired hypothesis test for short-read count data with small sample sizes
    DataMatrix Create DataMatrix object
    DataMatrix object Data structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
    NegativeBinomialTest Unpaired hypothesis test result

    Gene Ontology

    goannotread Read annotations from Gene Ontology annotated file
    num2goid Convert numbers to Gene Ontology IDs
    geneont Data structure containing Gene Ontology (GO) information

    Network Analysis and Visualization

    graphallshortestpaths Find all shortest paths in graph
    graphconncomp Find strongly or weakly connected components in graph
    graphisdag Test for cycles in directed graph
    graphisomorphism Find isomorphism between two graphs
    graphisspantree Determine if tree is spanning tree
    graphmaxflow Calculate maximum flow in directed graph
    graphminspantree Find minimal spanning tree in graph
    graphpred2path Convert predecessor indices to paths
    graphshortestpath Solve shortest path problem in graph
    graphtopoorder Perform topological sort of directed acyclic graph
    graphtraverse Traverse graph by following adjacent nodes
    biograph Create biograph object
    biograph object Data structure containing generic interconnected data used to implement directed graph

    Sequence Analysis

    Data Import and Export

    fastainfo Return information about FASTA file
    fastaread Read data from FASTA file
    fastawrite Write to file using FASTA format
    genbankread Read data from GenBank file
    getgenbank Retrieve sequence information from GenBank database
    genpeptread Read data from GenPept file
    getgenpept Retrieve sequence information from GenPept database
    emblread Read data from EMBL file
    getembl Retrieve sequence information from EMBL database
    pdbread Read data from Protein Data Bank (PDB) file
    pdbwrite Write to file using Protein Data Bank (PDB) format
    getpdb Retrieve protein structure data from Protein Data Bank (PDB) database
    fastqinfo Return information about FASTQ file
    fastqread Read data from FASTQ file
    fastqwrite Write to file using FASTQ format
    blastread Read data from NCBI BLAST report file
    blastreadlocal Read data from local BLAST report
    blastformat Create local BLAST database
    getblast Retrieve BLAST report from NCBI Web site
    multialignread Read multiple sequence alignment file
    multialignwrite Write multiple alignment to file
    pfamhmmread Read data from PFAM HMM-formatted file
    gethmmprof Retrieve hidden Markov model (HMM) profile from PFAM database
    gethmmtree Retrieve phylogenetic tree data from PFAM database
    gethmmalignment Retrieve multiple sequence alignment associated with hidden Markov model (HMM) profile from PFAM database
    phytreeread Read phylogenetic tree file
    phytreewrite Write phylogenetic tree object to Newick-formatted file

    Nucleotide Sequence Analysis

    basecount Count nucleotides in sequence
    codonbias Calculate codon frequency for each amino acid coded for in nucleotide sequence
    codoncount Count codons in nucleotide sequence
    dimercount Count dimers in nucleotide sequence
    ntdensity Plot density of nucleotides along sequence
    seqwordcount Count number of occurrences of word in sequence
    nt2aa Convert nucleotide sequence to amino acid sequence
    aa2nt Convert amino acid sequence to nucleotide sequence
    nt2int Convert nucleotide sequence from letter to integer representation
    int2nt Convert nucleotide sequence from integer to letter representation
    dna2rna Convert DNA sequence to RNA sequence
    rna2dna Convert RNA sequence to DNA sequence
    revgeneticcode Return reverse mapping (amino acid to nucleotide codon) for genetic code
    seqcomplement Calculate complementary strand of nucleotide sequence
    seqrcomplement Calculate reverse complementary strand of nucleotide sequence
    seqreverse Calculate reverse strand of nucleotide sequence
    baselookup Find nucleotide codes, integers, names, and complements
    geneticcode Return nucleotide codon to amino acid mapping for genetic code
    oligoprop Calculate sequence properties of DNA oligonucleotide
    cpgisland Locate CpG islands in DNA sequence
    joinseq Join two sequences to produce shortest supersequence
    palindromes Find palindromes in sequence
    randseq Generate random sequence from finite alphabet
    seqmatch Find matches for every string in library
    seqviewer Visualize and interactively explore biological sequences
    seqdisp Format long sequence output for easy viewing
    seqshoworfs Display open reading frames in sequence
    seqshowwords Graphically display words in sequence
    featuresmap Draw linear or circular map of features from GenBank structure
    featuresparse Parse features from GenBank, GenPept, or EMBL data
    seqconsensus Calculate consensus sequence
    seqdotplot Create dot plot of two sequences
    seqlogo Display sequence logo for nucleotide or amino acid sequences
    seqprofile Calculate sequence profile from set of multiply aligned sequences
    seqinsertgaps Insert gaps into nucleotide or amino acid sequence
    rebasecuts Find restriction enzymes that cut nucleotide sequence
    restrict Split nucleotide sequence at restriction site
    seq2regexp Convert sequence with ambiguous characters to regular expression

    Protein and Amino Acid Sequence Analysis

    aacount Count amino acids in sequence
    codonbias Calculate codon frequency for each amino acid coded for in nucleotide sequence
    codoncount Count codons in nucleotide sequence
    nmercount Count n-mers in nucleotide or amino acid sequence
    seqwordcount Count number of occurrences of word in sequence
    aa2nt Convert amino acid sequence to nucleotide sequence
    nt2aa Convert nucleotide sequence to amino acid sequence
    aa2int Convert amino acid sequence from letter to integer representation
    int2aa Convert amino acid sequence from integer to letter representation
    revgeneticcode Return reverse mapping (amino acid to nucleotide codon) for genetic code
    aminolookup Find amino acid codes, integers, abbreviations, names, and codons
    geneticcode Return nucleotide codon to amino acid mapping for genetic code
    atomiccomp Calculate atomic composition of protein
    isoelectric Estimate isoelectric point for amino acid sequence
    isotopicdist Calculate high-resolution isotope mass distribution and density function
    molweight Calculate molecular weight of amino acid sequence
    seqviewer Visualize and interactively explore biological sequences
    seqdisp Format long sequence output for easy viewing
    seqshoworfs Display open reading frames in sequence
    seqshowwords Graphically display words in sequence
    proteinplot Open Protein Plot window to investigate properties of amino acid sequence
    proteinpropplot Plot properties of amino acid sequence
    ramachandran Draw Ramachandran plot for Protein Data Bank (PDB) data
    seqconsensus Calculate consensus sequence
    seqdotplot Create dot plot of two sequences
    seqlogo Display sequence logo for nucleotide or amino acid sequences
    seqprofile Calculate sequence profile from set of multiply aligned sequences
    seqinsertgaps Insert gaps into nucleotide or amino acid sequence
    cleave Cleave amino acid sequence with enzyme
    cleavelookup Find cleavage rule for enzyme or compound
    seq2regexp Convert sequence with ambiguous characters to regular expression
    featuresparse Parse features from GenBank, GenPept, or EMBL data
    randseq Generate random sequence from finite alphabet
    seqmatch Find matches for every string in library

    Sequence Alignment

    localalign Return local optimal and suboptimal alignments between two sequences
    nwalign Globally align two sequences using Needleman-Wunsch algorithm
    swalign Locally align two sequences using Smith-Waterman algorithm
    seqdotplot Create dot plot of two sequences
    seqpdist Calculate pairwise distance between sequences
    seqalignviewer Visualize and edit multiple sequence alignment
    multialign Align multiple sequences using progressive method
    profalign Align two profiles using Needleman-Wunsch global alignment
    seqconsensus Calculate consensus sequence
    seqprofile Calculate sequence profile from set of multiply aligned sequences
    seqlogo Display sequence logo for nucleotide or amino acid sequences
    showalignment Display color-coded sequence alignment
    hmmprofalign Align query sequence to profile using hidden Markov model alignment
    hmmprofestimate Estimate profile hidden Markov model (HMM) parameters using pseudocounts
    hmmprofgenerate Generate random sequence drawn from profile hidden Markov model (HMM)
    hmmprofmerge Concatenate prealigned strings of several sequences to profile hidden Markov model (HMM)
    hmmprofstruct Create or edit hidden Markov model (HMM) profile structure
    showhmmprof Plot hidden Markov model (HMM) profile
    blastlocal Perform search on local BLAST database to create BLAST report
    blastncbi Create remote NCBI BLAST report request ID or link to NCBI BLAST report
    blosum Return BLOSUM scoring matrix
    dayhoff Return Dayhoff scoring matrix
    gonnet Return Gonnet scoring matrix
    nuc44 Return NUC44 scoring matrix for nucleotide sequences
    pam Return Point Accepted Mutation (PAM) scoring matrix

    Phylogenetic Analysis

    seqlinkage Construct phylogenetic tree from pairwise distances
    seqneighjoin Construct phylogenetic tree using neighbor-joining method
    seqpdist Calculate pairwise distance between sequences
    phytreeviewer Visualize, edit, and explore phylogenetic tree data
    dnds Estimate synonymous and nonsynonymous substitution rates
    dndsml Estimate synonymous and nonsynonymous substitution rates using maximum likelihood method
    gethmmtree Retrieve phylogenetic tree data from PFAM database
    seqinsertgaps Insert gaps into nucleotide or amino acid sequence
    phytree Create phytree object
    phytree object Data structure containing phylogenetic tree

    Structural Analysis

    rnaconvert Convert secondary structure of RNA sequence between bracket and matrix notations
    rnafold Predict minimum free-energy secondary structure of RNA sequence
    rnaplot Draw secondary structure of RNA sequence
    pdbtransform Apply linear transformation to 3-D structure of molecule
    pdbsuperpose Superpose 3-D structures of two proteins
    pdbread Read data from Protein Data Bank (PDB) file
    pdbwrite Write to file using Protein Data Bank (PDB) format
    molviewer Display and manipulate 3-D molecule structure
    pdbdistplot Visualize intermolecular distances in Protein Data Bank (PDB) file
    ramachandran Draw Ramachandran plot for Protein Data Bank (PDB) data
    evalrasmolscript Send RasMol script commands to Molecule Viewer window

    Mass Spectrometry and Bioanalytics

    Data Import

    mzcdfinfo Return information about netCDF file containing mass spectrometry data
    mzcdfread Read mass spectrometry data from netCDF file
    mzcdf2peaks Convert mzCDF structure to peak list
    mzxmlinfo Return information about mzXML file
    mzxmlread Read data from mzXML file
    mzxml2peaks Convert mzXML structure to peak list
    sffinfo Return information about SFF file
    sffread Read data from SFF file
    tgspcinfo Return information about SPC file
    tgspcread Read data from SPC file
    jcampread Read JCAMP-DX-formatted files
    scfread Read trace data from SCF file

    Preprocessing

    msresample Resample signal with peaks
    msbackadj Correct baseline of signal with peaks
    msnorm Normalize set of signals with peaks
    mslowess Smooth signal with peaks using nonparametric method
    mssgolay Smooth signal with peaks using least-squares polynomial
    msppresample Resample signal with peaks while preserving peaks
    msheatmap Create pseudocolor image of set of mass spectra
    msdotplot Plot set of peak lists from LC/MS or GC/MS data set
    msviewer Explore mass spectrum or set of mass spectra

    Spectrum and Signal Analysis

    mspeaks Convert raw peak data to peak list (centroided data)
    mspalign Align mass spectra from multiple peak lists from LC/MS or GC/MS data set
    msalign Align peaks in signal to reference peaks
    samplealign Align two data sets containing sequential observations by introducing gaps
    isotopicdist Calculate high-resolution isotope mass distribution and density function
    msheatmap Create pseudocolor image of set of mass spectra
    msdotplot Plot set of peak lists from LC/MS or GC/MS data set
    msviewer Explore mass spectrum or set of mass spectra
    traceplot Draw nucleotide trace plots
    metafeatures Attractor metagene algorithm for feature engineering using mutual information-based learning
    rankfeatures Rank key features by class separability criteria
    randfeatures Generate randomized subset of features
    fitcknn Fit k-nearest neighbor classifier
    classperf Evaluate performance of classifier
    crossvalind Generate cross-validation indices
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