changeset 8:6f010c2163c1 draft

Deleted selected files
author yufei-luo
date Wed, 23 Jan 2013 07:58:17 -0500
parents 839800dfba59
children a03838a6eb54
files DiffExpAnal/README.txt README.txt
diffstat 2 files changed, 0 insertions(+), 164 deletions(-) [+]
line wrap: on
line diff
--- a/DiffExpAnal/README.txt	Wed Jan 23 07:57:44 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-----------
-|  NAME  |
-----------
-Differential Expression Analysis Pipeline on RNA-Seq data
-
-
-Description
------------
-This pipeline has been founded by IBISA-APLIBIO(http://www.renabi.fr/platforms/aplibio/), 
-and has been built by (1)Yufei Luo, (2)Marie-Agnès Dillies, (1)Matthias Zytnicki and (1)Delphine Steinbach. 
-(1): Bioinformatics plateform URGI, INRA URGI Versailles, France
-(2): Plate-forme Transcriptome et Epigenome, Génopole, Institut Pasteur, France
-
-
-This pipeline performs differential expression analysis on two different conditions with arbitrary number of replicates.
-
-One reference genome (fasta format), one annotation (gtf format) and several RNA-seq samples are required.
-Step 0: Upload RNA-seq samples.
-Step 1: Clean the annotation file.
-Step 2: Clean the RNA-seq files.
-Step 3: Map the RNA-seq samples to the genome reference, using Tophat.
-Step 4: Convert the bam files (given by Tophat) to sam files.
-Step 5: Count the reads per annotation using S-MART (CompareOverlapping).
-Step 6: Build the input files for DESeq.
-Step 7: Differential expression analysis using DESeq, and output graphical results.
-
-More information about using this pipeline, please see: http://urgi.versailles.inra.fr/galaxy/u/yluo/p/differential-expression-pipeline-documentation
-
-
-Instructions
-------------
-Environment Installation:
-0). First, download and install S-MART (eg from Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart).
-1). Download and put the pipeline scripts directory under the S-MART directory
-    (ex. mv DiffExpAnal /home/user/galaxy-dist/tools/s_mart/SMART/.).
-
-Supplementary Softwares:
- * R, under the GNU General Public License (at least 2.14.1 version).
- * Python, under the Python License, compatible with the GNU General Public License (better 2.7)
- * S-MART (http://urgi.versailles.inra.fr/Tools/S-Mart), a toolbox which handles mapped RNA-Seq and ChIP-Seq data. 
- * DESeq (http://bioconductor.org/packages/release/bioc/html/DESeq.html), an R package to analyse
-   count data from high-throughput sequencing assays such as RNA-Seq and test
-   for differential expression. The package is available via Bioconductor (http://www.bioconductor.org/)
-   and can be conveniently installed as follows: 
-     Start an R session and type:
-     source("http://www.bioconductor.org/biocLite.R")
-     biocLite("DESeq")
- * Biobase(http://www.bioconductor.org/packages/2.12/bioc/html/Biobase.html), an
-   Bioconductor package and can be installed as follows:
-     source("http://bioconductor.org/biocLite.R")
-     biocLite("Biobase")
-
-
-Copyright
----------
-Copyright INRA-URGI 20012-2013
-
-
-Authors
--------
-Yufei Luo
-Marie-Agnès Dillies
-Matthias Zytnicki
-Delphine Steinbach
-
-
-Contact
--------
-urgi-support@versailles.inra.fr
-
-
-License
--------
-This library is distributed under the terms of the CeCILL license 
-(http://www.cecill.info/index.en.html).
-See the LICENSE.txt file.
-
-
-Acknowledgements
-----------------
-Yufei Luo was supported by the Plant Breeding and Genetics research division of
-the INRA, and by the Groupement d'intérêt scientifique IBISA.
--- a/README.txt	Wed Jan 23 07:57:44 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-----------
-|  NAME  |
-----------
-Differential Expression Analysis Pipeline on RNA-Seq data
-
-
-Description
------------
-This pipeline has been founded by IBISA-APLIBIO(http://www.renabi.fr/platforms/aplibio/), 
-and has been built by (1)Yufei Luo, (2)Marie-Agnès Dillies, (1)Matthias Zytnicki and (1)Delphine Steinbach. 
-(1): Bioinformatics plateform URGI, INRA URGI Versailles, France
-(2): Plate-forme Transcriptome et Epigenome, Génopole, Institut Pasteur, France
-
-
-This pipeline performs differential expression analysis on two different conditions with arbitrary number of replicates.
-
-One reference genome (fasta format), one annotation (gtf format) and several RNA-seq samples are required.
-Step 0: Upload RNA-seq samples.
-Step 1: Clean the annotation file.
-Step 2: Clean the RNA-seq files.
-Step 3: Map the RNA-seq samples to the genome reference, using Tophat.
-Step 4: Convert the bam files (given by Tophat) to sam files.
-Step 5: Count the reads per annotation using S-MART (CompareOverlapping).
-Step 6: Build the input files for DESeq.
-Step 7: Differential expression analysis using DESeq, and output graphical results.
-
-More information about using this pipeline, please see: http://urgi.versailles.inra.fr/galaxy/u/yluo/p/differential-expression-pipeline-documentation
-
-
-Instructions
-------------
-Environment Installation:
-0). First, download and install S-MART (eg from Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart).
-1). Download and put the pipeline scripts directory under the S-MART directory
-    (ex. mv DiffExpAnal /home/user/galaxy-dist/tools/s_mart/SMART/.).
-
-Supplementary Softwares:
- * R, under the GNU General Public License (at least 2.14.1 version).
- * Python, under the Python License, compatible with the GNU General Public License (better 2.7)
- * S-MART (http://urgi.versailles.inra.fr/Tools/S-Mart), a toolbox which handles mapped RNA-Seq and ChIP-Seq data. 
- * DESeq (http://bioconductor.org/packages/release/bioc/html/DESeq.html), an R package to analyse
-   count data from high-throughput sequencing assays such as RNA-Seq and test
-   for differential expression. The package is available via Bioconductor (http://www.bioconductor.org/)
-   and can be conveniently installed as follows: 
-     Start an R session and type:
-     source("http://www.bioconductor.org/biocLite.R")
-     biocLite("DESeq")
- * Biobase(http://www.bioconductor.org/packages/2.12/bioc/html/Biobase.html), an
-   Bioconductor package and can be installed as follows:
-     source("http://bioconductor.org/biocLite.R")
-     biocLite("Biobase")
-
-
-Copyright
----------
-Copyright INRA-URGI 20012-2013
-
-
-Authors
--------
-Yufei Luo
-Marie-Agnes Dillies
-Matthias Zytnicki
-Delphine Steinbach
-
-
-Contact
--------
-urgi-support@versailles.inra.fr
-
-
-License
--------
-This library is distributed under the terms of the CeCILL license 
-(http://www.cecill.info/index.en.html).
-See the LICENSE.txt file.
-
-
-Acknowledgements
-----------------
-Yufei Luo was supported by the Plant Breeding and Genetics research division of
-the INRA, and by the Groupement d'intérêt scientifique IBISA.