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Bioinformatics Toolbox Functions

Alphabetical List By Category
aa2int Convert amino acid sequence from letter to integer representation
aa2nt Convert amino acid sequence to nucleotide sequence
aacount Count amino acids in sequence
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
affyprobeseqread Read data file containing probe sequence information for Affymetrix GeneChip array
affyread Read microarray data from Affymetrix GeneChip file
affyrma Perform Robust Multi-array Average (RMA) procedure on Affymetrix microarray probe-level data
affysnpannotread Read Affymetrix Mapping DNA array data from CSV-format annotation file
affysnpintensitysplit Split Affymetrix SNP probe intensity information for alleles A and B
affysnpquartets Create table of SNP probe quartet results for Affymetrix probe set
agferead Read Agilent Feature Extraction Software file
align2cigar Convert aligned sequences to corresponding Compact Idiosyncratic Gapped Alignment Report (CIGAR) format
aminolookup Find amino acid codes, integers, abbreviations, names, and codons
atomiccomp Calculate atomic composition of protein
bamindexread Read Binary Sequence Alignment/Map Index (BAI) file
baminfo Return information about Binary Sequence Alignment/Map (BAM) file
bamread Read data from Binary Sequence Alignment/Map (BAM) file
basecount Count nucleotides in sequence
baselookup Find nucleotide codes, integers, names, and complements
biograph Create biograph object
biograph object Data structure containing generic interconnected data used to implement directed graph
BioIndexedFile Allow quick and efficient access to large text file with nonuniform-size entries Contain data values from microarray experiment Contain metadata from microarray experiment Contain experiment information from microarray gene expression experiment
bioma.ExpressionSet Contain data from microarray gene expression experiment
BioMap Contain sequence, quality, alignment, and mapping data
BioRead Contain sequence and quality data
BioReadQualityStatistics Quality statistics from a short-read sequence file
blastformat Create local BLAST database
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
blastread Read data from NCBI BLAST report file
blastreadlocal Read data from local BLAST report
blosum Return BLOSUM scoring matrix
bowtie Map short reads to reference sequence using Burrows-Wheeler transform
bowtiebuild Generate index using Burrows-Wheeler transform
celintensityread Read probe intensities from Affymetrix CEL files
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
cigar2align Convert unaligned sequences to aligned sequences using Compact Idiosyncratic Gapped Alignment Report (CIGAR) format
classperf Evaluate performance of classifier
cleave Cleave amino acid sequence with enzyme
cleavelookup Find cleavage rule for enzyme or compound
clustergram Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
clustergram object Object containing hierarchical clustering analysis data
codonbias Calculate codon frequency for each amino acid coded for in nucleotide sequence
codoncount Count codons in nucleotide sequence
cpgisland Locate CpG islands in DNA sequence
crossvalind Generate cross-validation indices
cytobandread Read cytogenetic banding information
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
dayhoff Return Dayhoff scoring matrix
dimercount Count dimers in nucleotide sequence
dna2rna Convert DNA sequence to RNA sequence
dnds Estimate synonymous and nonsynonymous substitution rates
dndsml Estimate synonymous and nonsynonymous substitution rates using maximum likelihood method
emblread Read data from EMBL file
evalrasmolscript Send RasMol script commands to Molecule Viewer window
exprprofrange Calculate range of gene expression profiles
exprprofvar Calculate variance of gene expression profiles
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
featurecount Compute the number of reads mapped to genomic features
featureparse Parse features from GenBank, GenPept, or EMBL data
featuresmap Draw linear or circular map of features from GenBank structure
featuresparse Parse features from GenBank, GenPept, or EMBL data
featureview Draw linear or circular map of features from GenBank structure
galread Read microarray data from GenePix array list file
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
genbankread Read data from GenBank file
geneentropyfilter Remove genes with low entropy expression values
genelowvalfilter Remove gene profiles with low absolute values
geneont Data structure containing Gene Ontology (GO) information
generangefilter Remove gene profiles with small profile ranges
geneticcode Return nucleotide codon to amino acid mapping for genetic code
genevarfilter Filter genes with small profile variance
genpeptread Read data from GenPept file
geoseriesread Read Gene Expression Omnibus (GEO) Series (GSE) format data
geosoftread Read Gene Expression Omnibus (GEO) SOFT format data
getblast Retrieve BLAST report from NCBI Web site
getembl Retrieve sequence information from EMBL database
getgenbank Retrieve sequence information from GenBank database
getgenpept Retrieve sequence information from GenPept database
getgeodata Retrieve Gene Expression Omnibus (GEO) format data
gethmmalignment Retrieve multiple sequence alignment associated with hidden Markov model (HMM) profile from PFAM database
gethmmprof Retrieve hidden Markov model (HMM) profile from PFAM database
gethmmtree Retrieve phylogenetic tree data from PFAM database
getpdb Retrieve protein structure data from Protein Data Bank (PDB) database
GFFAnnotation Represent General Feature Format (GFF) annotations
goannotread Read annotations from Gene Ontology annotated file
gonnet Return Gonnet scoring matrix
gprread Read microarray data from GenePix Results (GPR) file
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
GTFAnnotation Represent Gene Transfer Format (GTF) annotations
HeatMap Display heat map of matrix data and create HeatMap object
HeatMap object Object containing matrix and heat map display properties
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 Displays a set of HMM profile alignments
hmmprofstruct Create or edit hidden Markov model (HMM) profile structure
ilmnbslookup Look up Illumina BeadStudio target (probe) sequence and annotation information
ilmnbsread Read gene expression data exported from Illumina BeadStudio software
imageneread Read microarray data from ImaGene Results file
int2aa Convert amino acid sequence from integer to letter representation
int2nt Convert nucleotide sequence from integer to letter representation
isoelectric Estimate isoelectric point for amino acid sequence
isotopicdist Calculate high-resolution isotope mass distribution and density function
jcampread Read JCAMP-DX-formatted files
joinseq Join two sequences to produce shortest supersequence
knnimpute Impute missing data using nearest-neighbor method
localalign Return local optimal and suboptimal alignments between two sequences
maboxplot Create box plot for microarray data
mafdr Estimate false discovery rate (FDR) for multiple hypothesis testing
magetfield Extract data from microarray structure
maimage Spatial image for microarray data
mainvarsetnorm Perform rank invariant set normalization on gene expression values from two experimental conditions or phenotypes
mairplot Create intensity versus ratio scatter plot of microarray data
maloglog Create loglog plot of microarray data
malowess Smooth microarray data using Lowess method
manorm Normalize microarray data
mapcaplot Create Principal Component Analysis (PCA) plot of microarray data
mattest Perform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mavolcanoplot Create significance versus gene expression ratio (fold change) scatter plot of microarray data
metafeatures Attractor metagene algorithm for feature engineering using mutual information-based learning
microplateplot Display visualization of microtiter plate
molviewer Display and manipulate 3-D molecule structure
molweight Calculate molecular weight of amino acid sequence
msalign Align peaks in signal to reference peaks
msbackadj Correct baseline of signal with peaks
msdotplot Plot set of peak lists from LC/MS or GC/MS data set
msheatmap Create pseudocolor image of set of mass spectra
mslowess Smooth signal with peaks using nonparametric method
msnorm Normalize set of signals with peaks
mspalign Align mass spectra from multiple peak lists from LC/MS or GC/MS data set
mspeaks Convert raw peak data to peak list (centroided data)
msppresample Resample signal with peaks while preserving peaks
msresample Resample signal with peaks
mssgolay Smooth signal with peaks using least-squares polynomial
msviewer Explore mass spectrum or set of mass spectra
multialign Align multiple sequences using progressive method
multialignread Read multiple sequence alignment file
multialignwrite Write multiple alignment to file
mzcdf2peaks Convert mzCDF structure to peak list
mzcdfinfo Return information about netCDF file containing mass spectrometry data
mzcdfread Read mass spectrometry data from netCDF file
mzxml2peaks Convert mzXML structure to peak list
mzxmlinfo Return information about mzXML file
mzxmlread Read data from mzXML file
nbintest Unpaired hypothesis test for short-read count data with small sample sizes
ngsbrowser Open NGS Browser to visualize and explore short-read sequence alignments
nmercount Count n-mers in nucleotide or amino acid sequence
nt2aa Convert nucleotide sequence to amino acid sequence
nt2int Convert nucleotide sequence from letter to integer representation
ntdensity Plot density of nucleotides along sequence
nuc44 Return NUC44 scoring matrix for nucleotide sequences
num2goid Convert numbers to Gene Ontology IDs
nwalign Globally align two sequences using Needleman-Wunsch algorithm
oligoprop Calculate sequence properties of DNA oligonucleotide
palindromes Find palindromes in sequence
pam Return Point Accepted Mutation (PAM) scoring matrix
pdbdistplot Visualize intermolecular distances in Protein Data Bank (PDB) file
pdbread Read data from Protein Data Bank (PDB) file
pdbsuperpose Superpose 3-D structures of two proteins
pdbtransform Apply linear transformation to 3-D structure of molecule
pdbwrite Write to file using Protein Data Bank (PDB) format
pfamhmmread Read data from PFAM HMM-formatted file
phytree Create phytree object
phytree object Data structure containing phylogenetic tree
phytreeread Read phylogenetic tree file
phytreeviewer Visualize, edit, and explore phylogenetic tree data
phytreewrite Write phylogenetic tree object to Newick-formatted file
probelibraryinfo Create table of probe set library information
probesetlink Display probe set information on NetAffx Web site
probesetlookup Look up information for Affymetrix probe set
probesetplot Plot Affymetrix probe set intensity values
probesetvalues Create table of Affymetrix probe set intensity values
profalign Align two profiles using Needleman-Wunsch global alignment
proteinplot Open Protein Plot window to investigate properties of amino acid sequence
proteinpropplot Plot properties of amino acid sequence
quantilenorm Quantile normalization over multiple arrays
ramachandran Draw Ramachandran plot for Protein Data Bank (PDB) data
randfeatures Generate randomized subset of features
randseq Generate random sequence from finite alphabet
rankfeatures Rank key features by class separability criteria
rebasecuts Find restriction enzymes that cut nucleotide sequence
redbluecmap Create red and blue colormap
redgreencmap Create red and green colormap
restrict Split nucleotide sequence at restriction site
revgeneticcode Return reverse mapping (amino acid to nucleotide codon) for genetic code
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
rna2dna Convert RNA sequence to DNA sequence
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
saminfo Return information about Sequence Alignment/Map (SAM) file
samplealign Align two data sets containing sequential observations by introducing gaps
samread Read data from Sequence Alignment/Map (SAM) file
scfread Read trace data from SCF file
seq2regexp Convert sequence with ambiguous characters to regular expression
seqalignviewer Visualize and edit multiple sequence alignment
seqcomplement Calculate complementary strand of nucleotide sequence
seqconsensus Calculate consensus sequence
seqdisp Format long sequence output for easy viewing
seqdotplot Create dot plot of two sequences
seqfilter Filter out sequences based on specified criterion
seqinsertgaps Insert gaps into nucleotide or amino acid sequence
seqlinkage Construct phylogenetic tree from pairwise distances
seqlogo Display sequence logo for nucleotide or amino acid sequences
seqmatch Find matches for every character vector in library
seqneighjoin Construct phylogenetic tree using neighbor-joining method
seqpdist Calculate pairwise distance between sequences
seqprofile Calculate sequence profile from set of multiply aligned sequences
seqqcplot Create quality control plots for sequence and quality data
seqrcomplement Calculate reverse complementary strand of nucleotide sequence
seqreverse Calculate reverse strand of nucleotide sequence
seqshoworfs Display open reading frames in sequence
seqshowwords Graphically display words in sequence
seqsplit Split sequences into separate files based on barcodes
seqsplitpe Split merged paired-end sequences into separate files
seqtrim Trim sequences based on specified criterion
seqviewer Visualize and interactively explore biological sequences
seqwordcount Count number of occurrences of word in sequence
sffinfo Return information about SFF file
sffread Read data from SFF file
showalignment Display color-coded sequence alignment
showhmmprof Plot hidden Markov model (HMM) profile
soapread Read data from Short Oligonucleotide Analysis Package (SOAP) file
sptread Read data from SPOT file
swalign Locally align two sequences using Smith-Waterman algorithm
tgspcinfo Return information about SPC file
tgspcread Read data from SPC file
traceplot Draw nucleotide trace plots
zonebackadj Perform background adjustment on Affymetrix microarray probe-level data using zone-based method
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