RNASeq

Code for storing and analyzing RNASeq data. Developed by Warmflash lab at Rice University.

Data classes

Sample - store data from one RNASeq sample MappedSample - subclass of sample. store one sample mapped to a reference database RNASeqData - store one dataset (typically one experiment) Emsembl - store an ensembl database

Useful analyses

RNASeqData.getExpressionByName get expression of all genes matching a particular string, across dataset RNASeqData.differentialExpression perform differential expression analysis across samples in a dataset

data storage functions

MappedSample - constructor maps the data from sample to an ensembl database Ensembl - constructor converts file downloaded from ensembl to an Ensembl object

Example scripts

makeNewDatasetObjects - shows how to create an RNASeqData object from one experiment