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Hierarchical Bayesian Analysis of Differential Expression and ALternative Splicing (HBA-DEALS)
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HBA-DEALS simultaneously characterizes differential expression and splicing in cohorts. 

HBA-DEALS is based on a hierarchical Bayesian model of the absolute expression levels of the gene 
and its isoforms. HBA-DEALS assumes that the data are available from *n* RNA-seq samples and that 
the sequence reads have been mapped to isoforms. The *n* samples are divided into two cohorts 
*n1* and *n2* (e.g., cases and controls). The output of any isoform quantification tool, 
including but not limited to `Salmon <https://pubmed.ncbi.nlm.nih.gov/28263959/>`_, 
`RSEM <https://pubmed.ncbi.nlm.nih.gov/21816040/>`_, `Kallisto <https://pubmed.ncbi.nlm.nih.gov/27043002/>`_, 
and `StringTie <https://pubmed.ncbi.nlm.nih.gov/25690850/>`_, can be used 
as the input for HBA-DEALS. 



.. figure:: /img/hbadeals.png
   :width: 70%
   :align: center



This documentation explains how to setup and run HBA-DEALS.



.. toctree::
   :maxdepth: 1
   :caption: Contents:

   setup
   cohort
   transcriptome
   hbadeals