Changelog and Updates

[jwinter6]

Version 1.40 (latest)

• added new library interface for pre-selection of screens
• added pre-made library re-evaluation for addgene-provide libraries
• fixed smaller bugs
• speed increase for some functions
• improved essential genes information
• added Advanced Options to skip FASTQ Quality Report, create own regular expression, use bad-quality libraries

Version 1.20

• updated FASTA files
• added advanced function such as slow FASTQ processing, no FAST quality report or the removal of low-quality data
• added pre-made sgRNA reannotation files for supported Addgene libraries -> no waiting anymore for sgRNA re-evaluation!
• increased overall speed
• implemented essential gene information, now you can easily check if ur screening worked out of the box with essential genes
• implemented various user feedback
• new sample dataset (available soon) with updated youtube videos
• switched to new port on docker: 8000, please check the readme!
• added multiple user functionality -> now more than one user can simultanouesly work!

Version 1.17

• fixed BAGEL issues
• added the possibility to download all data from the DATA REVIEW tab
• improved the performance ovberall
• replaced FASTQ handling by new FASTQ and SAM parser based oN RUST -> speed increase by 6x!
• improved report
• added Visualization of GenomeCRISPR data in Hit Confirmation -> Gene Overview
• added Essential / Non-essential gene Read count in Quality Control
• added Essential/non-essential Log2 FC in Hit Calling section -> you can compare the effect to any published CRISPR screened cell line in GenomeCRISPR

Version 1.16

• implemented raised issues (expert options, easier usage of custom regular expression, overriding low alignment warning)
• implemented much faster FASTQ data handling (speed improvement by 14x) -> see https://github.com/OliPelz/fastq_extractor_proof_of_principle/tree/master/extractor_in_RUST
• added new GenomeCRISPR plots for easier/faster visualization of data present in the GenomeCRISPR database
• fixed some issues with the report generation in rare cases
• added StringDB information as a plot in the Gene Enrichment
• added possibility to select TOP enriched/depleted/essential genes for Gene Set Enrichment
• added possibility to download LOG files (Docker Version only)
• general speed improvement
• added GenomeCRISPR overview plots in addition to tables
• added DAISY Essential/non-Essential Read Count information in QC section -> by this users can directly see of read count of essential/non-essentials are different (should be at a certain timepoint)

Version 1.14 (latest)

• source code added for release
• fixed typos
• enhanced stability of report generation

Version 1.12

• fixed glitch that caused crash after analysis

Version 1.11

• added more detailed error handling
• changed behaviour of automatic file renaming
• fixed rare BAGEL/ScreenBEAM issues
• added download of Hit Calling Data (Data Review Section) as Tab-separated .TSV or Excel .XLSX
• added download of sgRNA re-evaluation file (Data Review Section) as Tab-separated .TSV
• added CDF (cumulative frequency) plots for Gene and sgRNA level (takes long time to be visualized for Genome-wide screens and many samples!)
• reworked Data Review Section to be more user-friendly
• updated highcharts plots to latest version
• improved data handling for less hard disk space
• improved plot handling by adding crosshair/removing tooltips where applicable
• added Data Review Section to report
• improved speed of report generation
• improved UI for easier and more streamlined appearance
• fixed small glitches with libraries
• improved file consistency check even more - now even rare cases should be reported
• improved data handling to automatically correct certain flaws in file consistency to not interrupt the user experience
• improved error handling for sgRNA re-evaluation
• increased speed of plots Version 1.10
• added possibility to have log files exported in real time for debugging using -v parameter (see bottom of the page for debugging section)
• added status information on the Download CRISPRAnalyzeR page to show what features are active/inactive
• added additional error message for data mapping using bowtie2, so users now see what is the exact issue
• FASTQ options only display in case FASTQ.gz files have been uploaded

Version 1.09

• fixed glitches in data handling for Gene Overview section
• fixed proxy/no proxy issues
• added another progress bar to highlight sgRNA re-evaluation status
• added short help GIF animation to show how to adjust FASTQ regular expressions
• streamlined code

Version 1.08

• fixed rare internet connectivity issues
• updated filename handling -> automatically removes unwanted characters
• updated libraries

Version 1.07 (outdated)

• fixed report crashing

Version 1.04 (outdated)

Version 1.01 (outdated)

Version 0.99 (outdated)