Recent changes to ImReP tutorial

ImReP tutorial modified by Igor Mandric

Igor Mandric — Mon, 21 Nov 2016 06:02:18 -0000

--- v9
+++ v10
@@ -6,6 +6,7 @@

 In this tutorial we provide instructions on how to install and run the tool, as well how to interpret and use its output. 

+* [What is ImReP?](https://sourceforge.net/p/imrep/wiki/What%20is%20ImReP%3F/)
 * [Installation instructions](https://sourceforge.net/p/imrep/wiki/Installation%20instructions/)
 * [Running ImReP](https://sourceforge.net/p/imrep/wiki/Running%20ImReP/)
 * [ImReP input](https://sourceforge.net/p/imrep/wiki/ImReP%20input/)

ImReP tutorial modified by Igor Mandric

Igor Mandric — Mon, 21 Nov 2016 05:50:00 -0000

ImRep tutorial modified by Igor Mandric

Igor Mandric — Mon, 21 Nov 2016 05:46:45 -0000

--- v7
+++ v8
@@ -5,10 +5,12 @@
 We assume you have a basic knowledge of sequence analysis and of Unix-based operating systems (although you should be able to run the pipeline on MacOS, some commands may require modification). If you have limited knowledge of UNIX, we encourage you to follow the [Unix Tutorial](https://github.com/smangul1/rop/wiki/UNIX-Tutorial).

 In this tutorial we provide instructions on how to install and run the tool, as well how to interpret and use its output. 
+
 * [Installation instructions](https://sourceforge.net/p/imrep/wiki/Installation%20instructions/)
 * [Running ImReP](https://sourceforge.net/p/imrep/wiki/Running%20ImReP/)
 * [ImReP input](https://sourceforge.net/p/imrep/wiki/ImReP%20input/)
 * [Examples](https://sourceforge.net/p/imrep/wiki/Examples/)
 * [ImReP output](https://sourceforge.net/p/imrep/wiki/ImReP%20output/)

+
 Please do not hesitate to contact us (imandric1@student.gsu.edu, smangul@ucla.edu) if you have any comments, suggestions, or clarification requests regarding the tutorial or if you would like to contribute to this resource.

ImRep tutorial modified by Igor Mandric

Igor Mandric — Mon, 21 Nov 2016 05:45:51 -0000

--- v6
+++ v7
@@ -7,8 +7,8 @@
 In this tutorial we provide instructions on how to install and run the tool, as well how to interpret and use its output. 
 * [Installation instructions](https://sourceforge.net/p/imrep/wiki/Installation%20instructions/)
 * [Running ImReP](https://sourceforge.net/p/imrep/wiki/Running%20ImReP/)
-* [ImReP input|imrep-input](https://sourceforge.net/p/imrep/wiki/ImReP%20input/)
+* [ImReP input](https://sourceforge.net/p/imrep/wiki/ImReP%20input/)
 * [Examples](https://sourceforge.net/p/imrep/wiki/Examples/)
-* [ImReP output|imrep-output](https://sourceforge.net/p/imrep/wiki/ImReP%20output/)
+* [ImReP output](https://sourceforge.net/p/imrep/wiki/ImReP%20output/)

 Please do not hesitate to contact us (imandric1@student.gsu.edu, smangul@ucla.edu) if you have any comments, suggestions, or clarification requests regarding the tutorial or if you would like to contribute to this resource.

ImRep tutorial modified by Igor Mandric

Igor Mandric — Fri, 18 Nov 2016 07:39:55 -0000

--- v5
+++ v6
@@ -7,8 +7,8 @@
 In this tutorial we provide instructions on how to install and run the tool, as well how to interpret and use its output. 
 * [Installation instructions](https://sourceforge.net/p/imrep/wiki/Installation%20instructions/)
 * [Running ImReP](https://sourceforge.net/p/imrep/wiki/Running%20ImReP/)
-* [[ImReP input|imrep-input]]
+* [ImReP input|imrep-input](https://sourceforge.net/p/imrep/wiki/ImReP%20input/)
 * [Examples](https://sourceforge.net/p/imrep/wiki/Examples/)
-* [[ImReP output|imrep-output]]
+* [ImReP output|imrep-output](https://sourceforge.net/p/imrep/wiki/ImReP%20output/)

 Please do not hesitate to contact us (imandric1@student.gsu.edu, smangul@ucla.edu) if you have any comments, suggestions, or clarification requests regarding the tutorial or if you would like to contribute to this resource.

ImRep tutorial modified by Igor Mandric

Igor Mandric — Fri, 18 Nov 2016 07:38:49 -0000

--- v4
+++ v5
@@ -8,7 +8,7 @@
 * [Installation instructions](https://sourceforge.net/p/imrep/wiki/Installation%20instructions/)
 * [Running ImReP](https://sourceforge.net/p/imrep/wiki/Running%20ImReP/)
 * [[ImReP input|imrep-input]]
-* [[Examples|examples]]
+* [Examples](https://sourceforge.net/p/imrep/wiki/Examples/)
 * [[ImReP output|imrep-output]]

 Please do not hesitate to contact us (imandric1@student.gsu.edu, smangul@ucla.edu) if you have any comments, suggestions, or clarification requests regarding the tutorial or if you would like to contribute to this resource.

ImRep tutorial modified by Igor Mandric

Igor Mandric — Fri, 18 Nov 2016 07:35:44 -0000

--- v3
+++ v4
@@ -6,7 +6,7 @@

 In this tutorial we provide instructions on how to install and run the tool, as well how to interpret and use its output. 
 * [Installation instructions](https://sourceforge.net/p/imrep/wiki/Installation%20instructions/)
-* [[Running ImReP|running-imrep]]
+* [Running ImReP](https://sourceforge.net/p/imrep/wiki/Running%20ImReP/)
 * [[ImReP input|imrep-input]]
 * [[Examples|examples]]
 * [[ImReP output|imrep-output]]

ImRep tutorial modified by Igor Mandric

Igor Mandric — Fri, 18 Nov 2016 07:34:55 -0000

--- v2
+++ v3
@@ -5,7 +5,7 @@
 We assume you have a basic knowledge of sequence analysis and of Unix-based operating systems (although you should be able to run the pipeline on MacOS, some commands may require modification). If you have limited knowledge of UNIX, we encourage you to follow the [Unix Tutorial](https://github.com/smangul1/rop/wiki/UNIX-Tutorial).

 In this tutorial we provide instructions on how to install and run the tool, as well how to interpret and use its output. 
-* [[Installation instructions|installation-instructions]]
+* [Installation instructions](https://sourceforge.net/p/imrep/wiki/Installation%20instructions/)
 * [[Running ImReP|running-imrep]]
 * [[ImReP input|imrep-input]]
 * [[Examples|examples]]

ImRep tutorial modified by Igor Mandric

Igor Mandric — Fri, 18 Nov 2016 07:32:35 -0000

--- v1
+++ v2
@@ -1,8 +1,14 @@
-Welcome to your wiki!
+#ImReP tutorial

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+ImReP is a tool written in Python programming language (version 2.7) which is designed to assemble CDR3 region sequences from RNA- or TCR-(BCR-)-Seq reads (either single- or paired-end) and provide immune repertoire as a set of clonotypes with their counts. 

-The wiki uses [Markdown](/p/imrep/wiki/markdown_syntax/) syntax.
+We assume you have a basic knowledge of sequence analysis and of Unix-based operating systems (although you should be able to run the pipeline on MacOS, some commands may require modification). If you have limited knowledge of UNIX, we encourage you to follow the [Unix Tutorial](https://github.com/smangul1/rop/wiki/UNIX-Tutorial). 

-[[members limit=20]]
-[[download_button]]
+In this tutorial we provide instructions on how to install and run the tool, as well how to interpret and use its output. 
+* [[Installation instructions|installation-instructions]]
+* [[Running ImReP|running-imrep]]
+* [[ImReP input|imrep-input]]
+* [[Examples|examples]]
+* [[ImReP output|imrep-output]]
+
+Please do not hesitate to contact us (imandric1@student.gsu.edu, smangul@ucla.edu) if you have any comments, suggestions, or clarification requests regarding the tutorial or if you would like to contribute to this resource.

ImRep tutorial modified by Igor Mandric

Igor Mandric — Fri, 18 Nov 2016 07:31:25 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

Igor Mandric (admin)