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.
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 | Two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes |
mafdr | Estimate positive false discovery rate for multiple 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 (Since R2021b) |
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 for cuffcompare |
CuffDiffOptions | Option set for cuffdiff |
CuffGFFReadOptions | Option set for cuffgffread |
CufflinksOptions | Option set for cufflinks |
CuffMergeOptions | Option set for cuffmerge |
CuffNormOptions | Option set for cuffnorm |
CuffQuantOptions | Option set for cuffquant |
Topics
- Bioinformatics Toolbox Software Support Packages
Download and install Bioinformatics support packages for NGS workflows.