SageExpress - SAGE-seq EXPRESSion analysis pipelines

About

SAGE-Express is a package of pipelines to process SAGE-Seq high throughput gene expression data set. The pipelines are maily composed of 3 parts:

  1. Mapping of sense and antisense strands of mitochondrial and RefSeq genes;
  2. Library normalization using empirical Bayes method;
  3. Identification of differentially expressed genes. The package is written using python and R.

Features

  1. Tag mapping using SeqMap allowing mapping of sense and antisense strands of mitochondrial and RefSeq genes.
  2. Sequencing errors identifications and reduction using mapping information.
  3. Empirical Bayes correction for tag-based count normalization.
  4. Differentially gene analysis applying SAM algorithm.

Author

Z. Jeremy Wu from X. Shirley Liu's lab

jeremywu at jimmy dot harvard dot edu

Citation

License

This software is distributed under the terms of Artistic License