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Jan Winter
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updated README
added Report sample files
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README.md

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@@ -77,6 +77,9 @@ Finally you can document the screening data and analysis using the interactive r
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[![CRISPRAnalyzeR Report Preview](https://github.com/boutroslab/crispr-analyzer/blob/master/images/CRISPRAnalyzeR_YT_report1.png)](https://www.youtube.com/embed/eusAj4LrSik)
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---
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# How to download the CRISPRAnalyzeR
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#### You can also check our [live demo](http://crispr-analyzer.dkfz.de), which you can also use to analyse your screening data.
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- fixed some typos
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- fixed report generation issue with larger datasets
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Version 1.12
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- fixed glitch that caused crash after analysis
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Version 1.11
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- added more detailed error handling
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- changed behaviour of automatic file renaming
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- fixed rare BAGEL/ScreenBEAM issues
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- added download of Hit Calling Data (Data Review Section) as Tab-separated .TSV or Excel .XLSX
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- added download of sgRNA re-evaluation file (Data Review Section) as Tab-separated .TSV
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- added CDF (cumulative frequency) plots for Gene and sgRNA level (takes long time to be visualized for Genome-wide screens and many samples!)
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- reworked Data Review Section to be more user-friendly
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- updated highcharts plots to latest version
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- improved data handling for less hard disk space
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- improved plot handling by adding crosshair/removing tooltips where applicable
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- added Data Review Section to report
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- improved speed of report generation
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- improved UI for easier and more streamlined appearance
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- fixed small glitches with libraries
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- improved file consistency check even more - now even rare cases should be reported
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- improved data handling to automatically correct certain flaws in file consistency to not interrupt the user experience
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- improved error handling for sgRNA re-evaluation
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- increased speed of plots
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Version 1.10
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- added possibility to have log files exported in real time for debugging using -v parameter (see bottom of the page for debugging section)
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- added status information on the Download CRISPRAnalyzeR page to show what features are active/inactive
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- added additional error message for data mapping using bowtie2, so users now see what is the exact issue
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- FASTQ options only display in case FASTQ.gz files have been uploaded
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Version 1.09
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- fixed glitches in data handling for Gene Overview section
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- fixed proxy/no proxy issues
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- added another progress bar to highlight sgRNA re-evaluation status
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- added short help GIF animation to show how to adjust FASTQ regular expressions
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- streamlined code
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Version 1.08
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- fixed rare internet connectivity issues
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- updated filename handling -> automatically removes unwanted characters
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- updated libraries
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OLDER VERSIONS are not available anymore.
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```
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__ATTENTION__ In case you will see a red error message like `Could not connect to xxxx`, this is an indication that you are behind a proxy server which blocks the access!
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If this is the case, please use a network connection without a proxy OR follow the __[Installation Procedure for Advanced Users](https://github.com/boutroslab/CRISPRAnalyzeR#command-line-installation-advanced-users)__
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9. Select CREATE to install the latest stable version of CRISPRAnalyzeR to install CRISPRAnalyzeR
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9. __Select CREATE__ to install the latest stable version of CRISPRAnalyzeR to install CRISPRAnalyzeR
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10. __OPTIONAL__ If required, you can adjust a couple of parameters, such as a proxy server.
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All parameters are described in more detail __[below](https://github.com/boutroslab/CRISPRAnalyzeR#available-paramaters-to-start-crispranalyzer)__
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To adjust these parameters, click on the __Settings__ tab on the upper right corner:
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![CA_url](https://github.com/boutroslab/crispr-analyzer/blob/master/images/CA_kitematic_URL.png)
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13. Now you successfully installed and started CRISPRAnalyzeR!
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13. __Now you successfully installed and started CRISPRAnalyzeR!__
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### How to Start, Stop or Restart CRISPRAnalyzeR
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Hit the __start, stop or restart__ button.
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![CA_overview](https://github.com/boutroslab/crispr-analyzer/blob/master/images/CA_kitematic_overview.png)
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### How to adjust the CRISPRAnalyzeR settings
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As mentioned [below](https://github.com/boutroslab/CRISPRAnalyzeR#available-paramaters-to-start-crispranalyzer), CRISPRAnalyzeR can be adjusted with several parameters.
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![CA_Options](https://github.com/boutroslab/crispr-analyzer/blob/master/images/CA_kitematic_settings.png)
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### Install specific version
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1. Search for CRISPRAnalyzeR in the Kitematic UI repository
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