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
- Bioinformatics Toolbox Software Support Packages
Download and install Bioinformatics support packages for NGS workflows.