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!!!ArrayExpressHTS R/Bioconductor based Package
;__ArrayExpressHTS__: ''is an R and Bioconductor RNA-seq processing pipeline that highly utilizes distributed computing for data processing and quality assessment of High-Throughput Sequencing experiments and datasets''

ArrayExpressHTS (AEHTS) is an R/Bioconductor-based pipeline for pre-processing, expression estimation and data quality assessment of RNA-seq datasets. It allow users to process FASTQ files into HTML quality reports and standard Bioconductor ExpressionSet objects that can be used for downstream analysis.

AEHTS works locally on a single computer or remotely on the EBI R cloud and can be used to analyse local datasets or public datasets from the ArrayExpress Archive of Functional Genomics Data at the EBI.

!!Overview of the pipeline
The pipeline starts from raw sequence files and produces standard Bioconductor R objects containing expression levels over features for downstream analysis, along with HTML reports for data quality assessment. Further informative intermediate data, such as alignment and annotation files, are also available.

__The different steps of the pipeline are:__
# Preparing the data and experimental metadata
# Generate a quality report
# Align to a reference
# Filter reads
# Generate an alignment report
# Estimate expression
# Generate a compared report

!!Contents of this documentation
* [ArrayExpressHTS Workflow|ArrayExpressHTS Workflow] 
* [Running AEHTS on the EBI R-Cloud|ArrayExpressHTS R-Cloud Configuration] 
** Find a dataset to analyse or upload your own data
** Launch the Workbench, register and create a new project 
** Run the whole pipeline with default options 
* [Installing and running AEHTS on a local computer|ArrayExpressHTS Local Configuration]
** [Pre-requisites|ArrayExpressHTS Local Configuration]
** [Preparing your own data|ArrayExpressHTS Data Preparation]
** [Preparing custom references|ArrayExpressHTS Custom References]
** [Running the pipeline|ArrayExpressHTS Local Configuration]
** [Re-running the pipeline|ArrayExpressHTS Re-running the Pipeline]
* [Advanced Configuration Options|ArrayExpressHTS Advanced Configuration Options]
** [Default options|ArrayExpressHTS Advanced Configuration Options]
** [Examples|ArrayExpressHTS Advanced Configuration Options]
* [Downstream Differential Expression Analysis|ArrayExpressHTS Differential Expression]

* [Example Quality Reports|ArrayExpressHTS Quality Reports]
* [Use cases|ArrayExpressHTS Use cases]
* [ArrayExpressHTS Workflow|ArrayExpressHTS Workflow] 



!!! Contact and help
Please use our mailing list: [http://listserver.ebi.ac.uk/mailman/listinfo/arrayexpresshts]