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Bioinformatics Toolbox Functions

Alphabetical List By Category

High-Throughput Sequencing

Data Import

fastainfoReturn information about FASTA file
fastareadRead data from FASTA file
fastawriteWrite to file using FASTA format
fastqinfoReturn information about FASTQ file
fastqreadRead data from FASTQ file
fastqwriteWrite to file using FASTQ format
saminfoReturn information about SAM file
samreadRead data from SAM file
baminfoReturn information about BAM file
bamreadRead data from BAM file
bamindexreadRead BAM Index, BAI, file
BioReadContain sequence and quality data
BioMapContain sequence, quality, alignment, and mapping data
BioReadQualityStatisticsQuality statistics from a short-read sequence file
BioIndexedFileAllow quick and efficient access to large text file with nonuniform-size entries
GFFAnnotationContain General Feature Format (GFF) annotations
GTFAnnotationContain Gene Transfer Format (GTF) annotations

Preprocessing

seqfilterFilter out sequences based on specified criterion
seqtrimTrim sequences based on specified criterion
seqsplitSplit sequences into separate files based on barcodes
seqsplitpeSplit merged paired-end sequences into separate files
seqqcplotCreate quality control plots for sequence and quality data

Alignment

bowtieMap short reads to reference sequence using Burrows-Wheeler transform
bowtiebuildGenerate index using Burrows-Wheeler transform
align2cigarConvert aligned sequences to corresponding signatures in CIGAR format
cigar2alignConvert unaligned sequences to aligned sequences using signatures in CIGAR format
BioMapContain sequence, quality, alignment, and mapping data

Statistical Analysis

mattestPerform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mafdrEstimate false discovery rate (FDR) for multiple hypothesis testing
nbintestUnpaired hypothesis test for count data with small sample sizes
featurecountCompute the number of reads mapped to genomic features
metafeaturesAttractor metagene algorithm for feature engineering using mutual information-based learning
rankfeaturesRank key features by class separability criteria
randfeaturesGenerate randomized subset of features
knnimputeImpute missing data using nearest-neighbor method
classperfEvaluate performance of classifier
crossvalindGenerate cross-validation indices
NegativeBinomialTestUnpaired hypothesis test result

Visualization

ngsbrowserOpen NGS Browser to visualize and explore alignments

Microarray Analysis

Data Import and Management

affyreadRead microarray data from Affymetrix GeneChip file
affysnpannotreadRead Affymetrix Mapping DNA array data from CSV-format annotation file
affyprobeseqreadRead data file containing probe sequence information for Affymetrix GeneChip array
celintensityreadRead probe intensities from Affymetrix CEL files
getgeodataRetrieve Gene Expression Omnibus (GEO) format data
geoseriesreadRead Gene Expression Omnibus (GEO) Series (GSE) format data
geosoftreadRead Gene Expression Omnibus (GEO) SOFT format data
galreadRead microarray data from GenePix array list file
gprreadRead microarray data from GenePix Results (GPR) file
agfereadRead Agilent Feature Extraction Software file
ilmnbsreadRead gene expression data exported from Illumina BeadStudio software
imagenereadRead microarray data from ImaGene Results file
sptreadRead data from SPOT file
goannotreadRead annotations from Gene Ontology annotated file
cytobandreadRead cytogenetic banding information
bioma.ExpressionSetContain data from microarray gene expression experiment
bioma.data.ExptDataContain data values from microarray experiment
bioma.data.MetaDataContain metadata from microarray experiment
bioma.data.MIAMEContain experiment information from microarray gene expression experiment

Preprocessing

affyrmaPerform Robust Multi-array Average (RMA) procedure on Affymetrix microarray probe-level data
affygcrmaPerform GC Robust Multi-array Average (GCRMA) procedure on Affymetrix microarray probe-level data
affyinvarsetnormPerform rank invariant set normalization on probe intensities from multiple Affymetrix CEL or DAT files
affyprobeaffinitiesCompute Affymetrix probe affinities from their sequences and MM probe intensities
affysnpintensitysplitSplit Affymetrix SNP probe intensity information for alleles A and B
affysnpquartetsCreate table of SNP probe quartet results for Affymetrix probe set
probesetvaluesCreate table of Affymetrix probe set intensity values
probesetlookupLook up information for Affymetrix probe set
probesetplotPlot Affymetrix probe set intensity values
probesetlinkDisplay probe set information on NetAffx Web site
probelibraryinfoCreate table of probe set library information
rmabackadjPerform background adjustment on Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure
rmasummaryCalculate gene expression values from Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure
gcrmaPerform GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization on Affymetrix microarray probe-level data
gcrmabackadjPerform GC Robust Multi-array Average (GCRMA) background adjustment on Affymetrix microarray probe-level data using sequence information
zonebackadjPerform background adjustment on Affymetrix microarray probe-level data using zone-based method
manormNormalize microarray data
quantilenormQuantile normalization over multiple arrays
mainvarsetnormPerform rank invariant set normalization on gene expression values from two experimental conditions or phenotypes
malowessSmooth microarray data using Lowess method
exprprofrangeCalculate range of gene expression profiles
exprprofvarCalculate variance of gene expression profiles
geneentropyfilterRemove genes with low entropy expression values
genelowvalfilterRemove gene profiles with low absolute values
generangefilterRemove gene profiles with small profile ranges
genevarfilterFilter genes with small profile variance
maimageSpatial image for microarray data
microplateplotDisplay visualization of microtiter plate
ilmnbslookupLook up Illumina BeadStudio target (probe) sequence and annotation information
magetfieldExtract data from microarray structure

Expression Analysis

mattestPerform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mafdrEstimate false discovery rate (FDR) for multiple hypothesis testing
mavolcanoplotCreate significance versus gene expression ratio (fold change) scatter plot of microarray data
mairplotCreate intensity versus ratio scatter plot of microarray data
maboxplotCreate box plot for microarray data
maloglogCreate loglog plot of microarray data
mapcaplotCreate Principal Component Analysis (PCA) plot of microarray data
nbintestUnpaired hypothesis test for count data with small sample sizes
clustergramCompute hierarchical clustering, display dendrogram and heat map, and create clustergram object
redbluecmapCreate red and blue colormap
redgreencmapCreate red and green colormap
probesetplotPlot Affymetrix probe set intensity values
metafeaturesAttractor metagene algorithm for feature engineering using mutual information-based learning
rankfeaturesRank key features by class separability criteria
randfeaturesGenerate randomized subset of features
knnimputeImpute missing data using nearest-neighbor method
classperfEvaluate performance of classifier
crossvalindGenerate cross-validation indices
DataMatrixCreate DataMatrix object
DataMatrix objectData structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
bioma.ExpressionSetContain data from microarray gene expression experiment
bioma.data.ExptDataContain data values from microarray experiment
bioma.data.MetaDataContain metadata from microarray experiment
bioma.data.MIAMEContain experiment information from microarray gene expression experiment
NegativeBinomialTestUnpaired hypothesis test result
HeatMapDisplay heat map of matrix data and create HeatMap object
HeatMap objectObject containing matrix and heat map display properties
clustergram objectObject containing hierarchical clustering analysis data

Genetic Variant Analysis

cghcbsPerform circular binary segmentation (CBS) on array-based comparative genomic hybridization (aCGH) data
cghfreqplotDisplay frequency of DNA copy number alterations across multiple samples
chromosomeplotPlot chromosome ideogram with G-banding pattern
gcrmaPerform GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization on Affymetrix microarray probe-level data
gcrmabackadjPerform GC Robust Multi-array Average (GCRMA) background adjustment on Affymetrix microarray probe-level data using sequence information
mattestPerform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mafdrEstimate false discovery rate (FDR) for multiple hypothesis testing
mavolcanoplotCreate significance versus gene expression ratio (fold change) scatter plot of microarray data
mairplotCreate intensity versus ratio scatter plot of microarray data
maboxplotCreate box plot for microarray data
maloglogCreate loglog plot of microarray data
mapcaplotCreate Principal Component Analysis (PCA) plot of microarray data
nbintestUnpaired hypothesis test for count data with small sample sizes
DataMatrixCreate DataMatrix object
DataMatrix objectData structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
NegativeBinomialTestUnpaired hypothesis test result

Gene Ontology

goannotreadRead annotations from Gene Ontology annotated file
num2goidConvert numbers to Gene Ontology IDs
geneontCreate geneont object and term objects

Network Analysis and Visualization

graphallshortestpathsFind all shortest paths in graph
graphconncompFind strongly or weakly connected components in graph
graphisdagTest for cycles in directed graph
graphisomorphismFind isomorphism between two graphs
graphisspantreeDetermine if tree is spanning tree
graphmaxflowCalculate maximum flow in directed graph
graphminspantreeFind minimal spanning tree in graph
graphpred2pathConvert predecessor indices to paths
graphshortestpathSolve shortest path problem in graph
graphtopoorderPerform topological sort of directed acyclic graph
graphtraverseTraverse graph by following adjacent nodes
biographCreate biograph object
biograph objectData structure containing generic interconnected data used to implement directed graph

Sequence Analysis

Data Import and Export

fastainfoReturn information about FASTA file
fastareadRead data from FASTA file
fastawriteWrite to file using FASTA format
genbankreadRead data from GenBank file
getgenbankRetrieve sequence information from GenBank database
genpeptreadRead data from GenPept file
getgenpeptRetrieve sequence information from GenPept database
emblreadRead data from EMBL file
getemblRetrieve sequence information from EMBL database
pdbreadRead data from Protein Data Bank (PDB) file
pdbwriteWrite to file using Protein Data Bank (PDB) format
getpdbRetrieve protein structure data from Protein Data Bank (PDB) database
fastqinfoReturn information about FASTQ file
fastqreadRead data from FASTQ file
fastqwriteWrite to file using FASTQ format
blastreadRead data from NCBI BLAST report file
blastreadlocalRead data from local BLAST report
blastformatCreate local BLAST database
getblastRetrieve BLAST report from NCBI website
multialignreadRead multiple sequence alignment file
multialignwriteWrite multiple alignment to file
pfamhmmreadRead data from PFAM HMM-formatted file
gethmmprofRetrieve hidden Markov model (HMM) profile from PFAM database
gethmmtreeRetrieve phylogenetic tree data from PFAM database
gethmmalignmentRetrieve multiple sequence alignment associated with hidden Markov model (HMM) profile from PFAM database
phytreereadRead phylogenetic tree file
phytreewriteWrite phylogenetic tree object to Newick-formatted file

Nucleotide Sequence Analysis

basecountCount nucleotides in sequence
codonbiasCalculate codon frequency for each amino acid coded for in nucleotide sequence
codoncountCount codons in nucleotide sequence
dimercountCount dimers in nucleotide sequence
ntdensityPlot density of nucleotides along sequence
seqwordcountCount number of occurrences of word in sequence
nt2aaConvert nucleotide sequence to amino acid sequence
aa2ntConvert amino acid sequence to nucleotide sequence
nt2intConvert nucleotide sequence from letter to integer representation
int2ntConvert nucleotide sequence from integer to letter representation
dna2rnaConvert DNA sequence to RNA sequence
rna2dnaConvert RNA sequence to DNA sequence
revgeneticcodeReturn reverse mapping (amino acid to nucleotide codon) for genetic code
seqcomplementCalculate complementary strand of nucleotide sequence
seqrcomplementCalculate reverse complementary strand of nucleotide sequence
seqreverseCalculate reverse strand of nucleotide sequence
baselookupFind nucleotide codes, integers, names, and complements
geneticcodeReturn nucleotide codon to amino acid mapping for genetic code
oligopropCalculate sequence properties of DNA oligonucleotide
cpgislandLocate CpG islands in DNA sequence
joinseqJoin two sequences to produce shortest supersequence
palindromesFind palindromes in sequence
randseqGenerate random sequence from finite alphabet
seqmatchFind matches for every character vector in library
seqviewerVisualize and interactively explore biological sequences
seqdispFormat long sequence output for easy viewing
seqshoworfsDisplay open reading frames in sequence
seqshowwordsGraphically display words in sequence
featuresmapDraw linear or circular map of features from GenBank structure
featureparseParse features from GenBank, GenPept, or EMBL data
featuresparseParse features from GenBank, GenPept, or EMBL data
featureviewDraw linear or circular map of features from GenBank structure
seqconsensusCalculate consensus sequence
seqdotplotCreate dot plot of two sequences
seqlogoDisplay sequence logo for nucleotide or amino acid sequences
seqprofileCalculate sequence profile from set of multiply aligned sequences
seqinsertgapsInsert gaps into nucleotide or amino acid sequence
rebasecutsFind restriction enzymes that cut nucleotide sequence
restrictSplit nucleotide sequence at restriction site
seq2regexpConvert sequence with ambiguous characters to regular expression

Protein and Amino Acid Sequence Analysis

aacountCount amino acids in sequence
codonbiasCalculate codon frequency for each amino acid coded for in nucleotide sequence
codoncountCount codons in nucleotide sequence
nmercountCount n-mers in nucleotide or amino acid sequence
seqwordcountCount number of occurrences of word in sequence
aa2ntConvert amino acid sequence to nucleotide sequence
nt2aaConvert nucleotide sequence to amino acid sequence
aa2intConvert amino acid sequence from letter to integer representation
int2aaConvert amino acid sequence from integer to letter representation
revgeneticcodeReturn reverse mapping (amino acid to nucleotide codon) for genetic code
aminolookupFind amino acid codes, integers, abbreviations, names, and codons
geneticcodeReturn nucleotide codon to amino acid mapping for genetic code
atomiccompCalculate atomic composition of protein
isoelectricEstimate isoelectric point for amino acid sequence
isotopicdistCalculate high-resolution isotope mass distribution and density function
molweightCalculate molecular weight of amino acid sequence
seqviewerVisualize and interactively explore biological sequences
seqdispFormat long sequence output for easy viewing
seqshoworfsDisplay open reading frames in sequence
seqshowwordsGraphically display words in sequence
proteinplotOpen Protein Plot window to investigate properties of amino acid sequence
proteinpropplotPlot properties of amino acid sequence
ramachandranDraw Ramachandran plot for Protein Data Bank (PDB) data
seqconsensusCalculate consensus sequence
seqdotplotCreate dot plot of two sequences
seqlogoDisplay sequence logo for nucleotide or amino acid sequences
seqprofileCalculate sequence profile from set of multiply aligned sequences
seqinsertgapsInsert gaps into nucleotide or amino acid sequence
cleaveCleave amino acid sequence with enzyme
cleavelookupFind cleavage rule for enzyme or compound
seq2regexpConvert sequence with ambiguous characters to regular expression
featuresparseParse features from GenBank, GenPept, or EMBL data
featureparseParse features from GenBank, GenPept, or EMBL data
randseqGenerate random sequence from finite alphabet
seqmatchFind matches for every character vector in library

Sequence Alignment

localalignReturn local optimal and suboptimal alignments between two sequences
nwalignGlobally align two sequences using Needleman-Wunsch algorithm
swalignLocally align two sequences using Smith-Waterman algorithm
seqdotplotCreate dot plot of two sequences
seqpdistCalculate pairwise distance between sequences
seqalignviewerVisualize and edit multiple sequence alignment
multialignAlign multiple sequences using progressive method
profalignAlign two profiles using Needleman-Wunsch global alignment
seqconsensusCalculate consensus sequence
seqprofileCalculate sequence profile from set of multiply aligned sequences
seqlogoDisplay sequence logo for nucleotide or amino acid sequences
showalignmentDisplay color-coded sequence alignment
hmmprofalignAlign query sequence to profile using hidden Markov model alignment
hmmprofestimateEstimate profile hidden Markov model (HMM) parameters using pseudocounts
hmmprofgenerateGenerate random sequence drawn from profile hidden Markov model (HMM)
hmmprofmergeDisplays a set of HMM profile alignments
hmmprofstructCreate or edit hidden Markov model (HMM) profile structure
showhmmprofPlot hidden Markov model (HMM) profile
blastlocalPerform search on local BLAST database to create BLAST report
blastncbiCreate remote NCBI BLAST report request ID or link to NCBI BLAST report
blosumReturn BLOSUM scoring matrix
dayhoffReturn Dayhoff scoring matrix
gonnetReturn Gonnet scoring matrix
nuc44Return NUC44 scoring matrix for nucleotide sequences
pamReturn Point Accepted Mutation (PAM) scoring matrix

Phylogenetic Analysis

seqlinkageConstruct phylogenetic tree from pairwise distances
seqneighjoinConstruct phylogenetic tree using neighbor-joining method
seqpdistCalculate pairwise distance between sequences
phytreeviewerVisualize, edit, and explore phylogenetic tree data
dndsEstimate synonymous and nonsynonymous substitution rates
dndsmlEstimate synonymous and nonsynonymous substitution rates using maximum likelihood method
gethmmtreeRetrieve phylogenetic tree data from PFAM database
seqinsertgapsInsert gaps into nucleotide or amino acid sequence
phytreeCreate phytree object
phytree objectData structure containing phylogenetic tree

Structural Analysis

RNA Secondary Structure Analysis

rnaconvertConvert secondary structure of RNA sequence between bracket and matrix notations
rnafoldPredict minimum free-energy secondary structure of RNA sequence
rnaplotDraw secondary structure of RNA sequence

Analysis of 3-D Structures of Biological Molecules

pdbtransformApply linear transformation to 3-D structure of molecule
pdbsuperposeSuperpose 3-D structures of two proteins
pdbreadRead data from Protein Data Bank (PDB) file
pdbwriteWrite to file using Protein Data Bank (PDB) format
molviewerDisplay and manipulate 3-D molecule structure
pdbdistplotVisualize intermolecular distances in Protein Data Bank (PDB) file
ramachandranDraw Ramachandran plot for Protein Data Bank (PDB) data
evalrasmolscriptSend RasMol script commands to Molecule Viewer window

Mass Spectrometry and Bioanalytics

Data Import

mzcdfinfoReturn information about netCDF file containing mass spectrometry data
mzcdfreadRead mass spectrometry data from netCDF file
mzcdf2peaksConvert mzCDF structure to peak list
mzxmlinfoReturn information about mzXML file
mzxmlreadRead data from mzXML file
mzxml2peaksConvert mzXML structure to peak list
sffinfoReturn information about SFF file
sffreadRead data from SFF file
tgspcinfoReturn information about SPC file
tgspcreadRead data from SPC file
jcampreadRead JCAMP-DX-formatted files
scfreadRead trace data from SCF file

Preprocessing

msresampleResample signal with peaks
msbackadjCorrect baseline of signal with peaks
msnormNormalize set of signals with peaks
mslowessSmooth signal with peaks using nonparametric method
mssgolaySmooth signal with peaks using least-squares polynomial
msppresampleResample signal with peaks while preserving peaks
msheatmapCreate pseudocolor image of set of mass spectra
msdotplotPlot set of peak lists from LC/MS or GC/MS data set
msviewerExplore mass spectrum or set of mass spectra

Spectrum and Signal Analysis

mspeaksConvert raw peak data to peak list (centroided data)
mspalignAlign mass spectra from multiple peak lists from LC/MS or GC/MS data set
msalignAlign peaks in signal to reference peaks
samplealignAlign two data sets containing sequential observations by introducing gaps
isotopicdistCalculate high-resolution isotope mass distribution and density function
msheatmapCreate pseudocolor image of set of mass spectra
msdotplotPlot set of peak lists from LC/MS or GC/MS data set
msviewerExplore mass spectrum or set of mass spectra
traceplotDraw nucleotide trace plots
metafeaturesAttractor metagene algorithm for feature engineering using mutual information-based learning
rankfeaturesRank key features by class separability criteria
randfeaturesGenerate randomized subset of features
classperfEvaluate performance of classifier
crossvalindGenerate cross-validation indices
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