ArrayExpressHTS R/Bioconductor based Package#
- 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
- Running AEHTS on the EBI R-Cloud
- 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
- Advanced Configuration Options
- Downstream Differential Expression Analysis
Contact and help#
Please use our mailing list: http://listserver.ebi.ac.uk/mailman/listinfo/arrayexpresshts
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« This particular version was published on 25-Jan-2011 11:39 by Andrew Tikhonov.