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This page was created on 04-Nov-2010 17:32 by Andrew Tikhonov

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__Would you like to try our new R-Cloud workbench?__
__Would you like to try our new R-Cloud Workbench?__
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Go to the [R Workbench Web Page|http://wwwdev.ebi.ac.uk/Tools/rcloud] and launch the latest version.
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 Package
!!!ArrayExpressHTS R/Bioconductor based Package
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ArrayExpressHTS is a distributed computing package for RNA-seq data processing and quality assessment for R/Bioconductor
;__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''
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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.
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.
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The different steps of the pipeline are:
__The different steps of the pipeline are:__
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* [Running AEHTS on the EBI R cloud|ArrayExpressHTS R-Cloud Configuration]
* [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
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* [Advanced configuration options|ArrayExpressHTS Advanced Configuration Options]
* [Example HTML quality reports|ArrayExpressHTS Quality Reports]
** [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]
\\
!!! Contact and help
\\
Please use our mailing list: [http://listserver.ebi.ac.uk/mailman/listinfo/arrayexpresshts]
Version Date Modified Size Author Changes ... Change note
19 10-Jul-2014 10:25 3.048 kB Andrew Tikhonov to previous
18 09-Jul-2014 18:35 3.345 kB AnonymousCoward35 to previous | to last
17 09-Jul-2014 18:34 3.283 kB AnonymousCoward to previous | to last
16 09-Jul-2014 18:29 3.222 kB AnonymousCoward32 to previous | to last
15 09-Jul-2014 18:26 3.159 kB AnonymousCoward2 to previous | to last
14 09-Jul-2014 18:25 3.1 kB AnonymousCoward to previous | to last
13 01-Feb-2012 16:36 3.046 kB Andrew Tikhonov to previous | to last
12 06-Oct-2011 11:59 2.99 kB Andrew Tikhonov to previous | to last
11 03-Jun-2011 14:25 2.934 kB Angela Goncalves to previous | to last
10 03-Jun-2011 14:18 2.926 kB Angela Goncalves to previous | to last
9 25-Jan-2011 11:53 2.807 kB Andrew Tikhonov to previous | to last
8 25-Jan-2011 11:50 2.807 kB Andrew Tikhonov to previous | to last
7 25-Jan-2011 11:39 2.718 kB Andrew Tikhonov to previous | to last
6 18-Jan-2011 23:11 2.704 kB Angela Goncalves to previous | to last
5 17-Dec-2010 11:15 2.71 kB Angela Goncalves to previous | to last
4 17-Dec-2010 01:47 2.639 kB Misha Kapushesky to previous | to last
3 10-Dec-2010 10:56 1.892 kB Angela Goncalves to previous | to last
2 04-Nov-2010 17:32 1.825 kB Andrew Tikhonov to previous | to last
1 04-Nov-2010 17:32 1.826 kB Andrew Tikhonov to last
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