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Go to the [R-Cloud Workbench Web Page|http://www.ebi.ac.uk/Tools/rcloud] and launch or install the latest version.
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!!!ArrayExpressHTS R/Bioconductor based Package
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;__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''

!!Purpose
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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
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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
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* [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] 

!!Downloads
[ArrayExpressHTS_1.0.tar.gz|http://www.ebi.ac.uk/Tools/rcloud/downloads/ArrayExpressHTS_1.0.tar.gz]

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