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This page (revision-14) was last changed on 10-Jul-2014 13:17 by Andrew Tikhonov

This page was created on 02-Jun-2011 09:10 by Rodrigo Santamaria

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At line 17 changed 3 lines
!!Overview of the pipeline
\\
The pipeline starts from raw CEL files located in a single folder and produces standard Bioconductor R objects containing expression levels after background correction, normalization and summarization via RMA.
!! Running aPE on the EBI R cloud
At line 21 removed 8 lines
__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
At line 30 removed 20 lines
!!Contents of this documentation
\\
* [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]
At line 51 changed one line
[ArrayExpressHTS_1.0.tar.gz|http://www.ebi.ac.uk/Tools/rcloud/downloads/ArrayExpressHTS_1.0.tar.gz]
[affyParaEBI_1.0.tar.gz|http://www.ebi.ac.uk/Tools/rcloud/downloads/affyParaEBI.tar.gz]
Version Date Modified Size Author Changes ... Change note
14 10-Jul-2014 13:17 3.621 kB Andrew Tikhonov to previous
13 10-Jul-2014 09:44 3.611 kB 172.18.6.30 to previous | to last
12 10-Jul-2014 09:40 3.647 kB 172.18.6.30 to previous | to last
11 25-Apr-2014 13:01 3.89 kB ZnivFv to previous | to last
10 27-Sep-2013 17:17 3.713 kB Andrew Tikhonov to previous | to last
9 10-Jan-2012 11:43 3.643 kB Andrew Tikhonov to previous | to last
8 02-Jun-2011 10:04 3.635 kB Rodrigo Santamaria to previous | to last
7 02-Jun-2011 09:58 3.647 kB Rodrigo Santamaria to previous | to last
6 02-Jun-2011 09:57 3.651 kB Rodrigo Santamaria to previous | to last
5 02-Jun-2011 09:50 3.662 kB Rodrigo Santamaria to previous | to last
4 02-Jun-2011 09:48 3.731 kB Rodrigo Santamaria to previous | to last
3 02-Jun-2011 09:34 0.931 kB Rodrigo Santamaria to previous | to last
2 02-Jun-2011 09:17 2.498 kB Rodrigo Santamaria to previous | to last
1 02-Jun-2011 09:10 1.787 kB Rodrigo Santamaria to last
« This page (revision-14) was last changed on 10-Jul-2014 13:17 by Andrew Tikhonov