Gene counts for interval data, coverage, alignment, and normalization; identification and visualization of differentially expressed genes and expression profiles; gene clustering by expression profiles


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
featurecount Compute the number of reads mapped to genomic features
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
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