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version 1.8.0 Rick Gelhausen Under construction

  • Added full support for paired-end data and mixed data (paired-end samples mixed with single-end samples)
  • paired-end data is now correctly trimmed, but will still be converted to single-end data due to lack of paired-end bam support of many downstream tools
  • Updated to version 8.10.7 of snakemake
  • Changed FileProviders to Storage
  • Fixed bug with blastDB generation in reparation
  • updated ReadTheDocs

version 1.7.1 Rick Gelhausen 23.06.2023

  • exchanged ftp server for swiss prot fasta download

version 1.7.0 Rick Gelhausen 24.02.2023

  • improved Snakefile and added validation for config file
  • updated config file structure
  • added 3D PCA plots for quality control
  • added 2D PCA plots + hierarchical clustering of read counts for quality control
  • fixed error that caused crashes when annotation had extra plasmids not present in genome file
  • updated manual
  • updated ReadTheDocs

version 1.6.2 Rick Gelhausen 04.10.2022

  • fixed bug where the new input tables were not correctly created depending on the input contrast.
  • fixed bug with wrong condition vector labeling causing incorrect behavior in riborex log2FC calculation
  • ensured that all three tools, deltaTE, riborex and xtail use the same orientation: treated vs untreated

version 1.6.1 Rick Gelhausen 29.09.2022

  • moved differential expression input creation to python to avoid compatability errors with new R versions.
  • fixed bug that caused overview_excel to fail when using differential expression

version 1.6.0 Rick Gelhausen 23.09.2022

  • fixed bug in metagene-profiling that caused negative strand not to be used correctly * fixed bug in metagene-profiling that caused negative strand not to be used correctly.
  • complete restructering of differential expression analysis
  • added deltaTE and re-added riborex
  • fixed issue with sorting between python and R
  • changed .xlsx format for differential expression, using sheets rather than multiple files.
  • cleaned differential expression scripts
  • added option to customize the input contrasts
  • updated tool versions to newest available

version 1.5.2 (added to 1.6.0) Rick Gelhausen -

  • removed riborex support and improved xtail support
  • fixed issue with missing xtail results in overview tables
  • added all annotated features to overview.xlsx
  • fixed bug where the min normalization was not correctly using the minimal value.
  • changed excel_writer to create xlsx files with freezed header
  • ensured correct sorting of xtail sorted files
  • fixed issue where xtail result tables had wrong naming
  • Changed naming of makereport.sh output files to ensure correct sorting

version 1.5.1 Rick Gelhausen & Florian Eggenhofer 28.07.2021

  • fixed issue which sometimes caused crashes in coverage file generation.
  • fixed versioning issues with snakemake and multiQC.
  • updated documentation + Manual

version 1.5.0 Rick Gelhausen & Florian Eggenhofer 09.06.2021

  • added improved meta gene profiling figures
  • added automatic detection of peak read lengths
  • added detection of best offset for individual readlengths
  • added pip packaging
  • functions organized in library
  • added old_locus_tag information to annotation excel files.
  • fixed a bug in the metagene-profiling that would cause a strange peak at the start/end for 5 or 3prime mappings.
  • improved the plot output for the metagene-profiling when checking many read lengths.
  • slightly changed the metagene-profiling read-counting to make it more comparable to the build in coverage files.
  • added metagene profiling for stop codons, this is automatically used on TTS and RNATTS libraries.

version 1.4.4 Rick Gelhausen & Florian Eggenhofer 18.09.2020

  • added overlap column to the overview table, to show whether an entry overlaps with an annotated gene.
  • improved the handling of TE wildcards in excel scripts, allowing input combinations that were previously not possible.
  • minor fix for mapping script that ensures the header is set correctly for the "mil" mapping.
  • minor fix that ensures the gene_name is set correctly and not sometimes replaced by the locus_tag.
  • fixed a bug where tranlation of nt_seqs were done only up to the first stop codon.
  • improved gtf2gff3 script to use gene_biotype to find RNA features.
  • improved start/stop gff files (including motifs and frames)
  • added 15nt upstream of the start codon to each .xlsx table.
  • updated reparation environment
  • some code clean-up

version 1.4.3 Rick Gelhausen & Florian Eggenhofer 15.05.2020

  • added genome-browser identifier to overview table
  • completely reworked gff2 support by transforming gff2 to gff3. This is unavoidable as some tools require gff3 format
  • added script to convert gff2 to gff3
  • improved overview table by adding and reordering columns
  • improved TE calculation to be less confusing, using NaN if read-counts are 0 and would lead to division by 0
  • improved excel file generation
  • resolved redundancies in excel files
  • updated manual + online documentation

version 1.4.2 Rick Gelhausen & Florian Eggenhofer 25.04.2020

  • fixed bug causing generate_overview_excel.py to crash for certain deepribo files
  • updated manual

version 1.4.1 Rick Gelhausen & Florian Eggenhofer 20.04.2020

  • added support for multi-condition results for differential expression in the overview table
  • updated manual

version 1.4.0 Rick Gelhausen & Florian Eggenhofer 17.04.2020

  • added overview table that aggregates all important information about ORFs
  • updated readcounting to consitently use the same method
  • updated makereport script
  • updated manual

version 1.3.2 Rick Gelhausen & Florian Eggenhofer 24.03.2020

  • updated sge.yaml
  • updated torque.yaml
  • bugfixed retrieveAnnotation
  • added xlsx output for xtail and riborex
  • added updated annotation containing reparation predictions and the orginal annotation
  • updated manual

version 1.3.1 Rick Gelhausen & Florian Eggenhofer 13.02.2020

  • added makereport script

version 1.3.0 Rick Gelhausen & Florian Eggenhofer 30.01.2020

  • integration of deepribo
  • added metagene profiling
  • added pseudogene read counting
  • refactoring of scripts folder
  • renamed summary.xlsx -> predictions_reparation.xlsx
  • removal of unneeded dependencies
  • Refactored Snakefiles

version 1.2.0 Rick Gelhausen & Florian Eggenhofer 22.01.2020

  • updated reparation to v1.0.9
  • added differential expression analysis with Riborex and Xtail
  • added TIS support to generate_excel.py
  • standardized output annotation to GFF3 format
  • updated HRIBO Manual

version 1.1.0 Rick Gelhausen & Florian Eggenhofer 22.08.2019

  • added paired-end support
  • paired-end mapping (currently no tools allowing this exist)
  • combined paired-end mapping
  • improved samples.xlsx (for paired end)
  • improved count_tables (rounding numbers to 2 floating points)
  • fix for annotation generation

version 1.0.0 Rick Gelhausen & Florian Eggenhofer 08.08.2019

  • initial commit