Main Content

Statistical Analysis

Read summarization and statistical analyses on RNA-seq and ChIP-seq data

Count the number of reads mapped to genomic features of interest. Perform statistical analyses on the read counts, such as identifying differentially expressed genes from RNA-Seq data, and performing genome-wide analysis of transcription factors from ChIP-Seq data.


cufflinksAssemble transcriptome from aligned reads (Since R2019a)
cuffcompareCompare assembled transcripts across multiple experiments (Since R2019a)
cuffdiffIdentify significant changes in transcript expression (Since R2019a)
cuffmergeMerge RNA-seq assemblies (Since R2019a)
cuffnormNormalize transcript expression levels (Since R2019a)
cuffquantQuantify gene and transcript expression profiles (Since R2019a)
cuffgffreadFilter and convert GFF and GTF files (Since R2019a)
cuffgtf2samConvert GTF files to SAM files (Since R2019a)
mattestPerform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mafdrEstimate positive false discovery rate 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
rnaseqdePerform differential expression analysis on RNA-seq count data (Since R2021b)
knnimputeImpute missing data using nearest-neighbor method
crossvalindGenerate indices for training and test sets
classperfEvaluate classifier performance


NegativeBinomialTestUnpaired hypothesis test result
CuffCompareOptionsOption set for cuffcompare (Since R2019a)
CuffDiffOptionsOption set for cuffdiff (Since R2019a)
CuffGFFReadOptionsOption set for cuffgffread (Since R2019a)
CufflinksOptionsOption set for cufflinks (Since R2019a)
CuffMergeOptionsOption set for cuffmerge (Since R2019a)
CuffNormOptionsOption set for cuffnorm (Since R2019a)
CuffQuantOptionsOption set for cuffquant (Since R2019a)