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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 asidentifying differentially expressed genesfrom RNA-seq data, and performinggenome-wide analysisof transcription factors from ChIP-seq data.

Functions

cufflinks Assemble transcriptome from aligned reads
cuffcompare Compare assembled transcripts across multiple experiments
cuffdiff Identify significant changes in transcript expression
cuffmerge Merge RNA-seq assemblies
cuffnorm Normalize transcript expression levels
cuffquant Quantify gene and transcript expression profiles
cuffgffread Filter and convert GFF and GTF files
cuffgtf2sam Convert GTF files to SAM files
mattest Perform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mafdr 估计multipl积极的错误发现率e hypothesis testing
nbintest Unpaired hypothesis test for count data with small sample sizes
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
rnaseqde Perform differential expression analysis on RNA-seq count data
knnimpute Impute missing data using nearest-neighbor method
crossvalind Generate indices for training and test sets
classperf Evaluate classifier performance

Classes

NegativeBinomialTest Unpaired hypothesis test result
CuffCompareOptions Option set forcuffcompare
CuffDiffOptions Option set forcuffdiff
CuffGFFReadOptions Option set forcuffgffread
CufflinksOptions Option set forcufflinks
CuffMergeOptions Option set forcuffmerge
CuffNormOptions Option set forcuffnorm
CuffQuantOptions Option set forcuffquant

Topics