sequana/sequana issues and pull requests

#762 - add fisher test in variant calling

Pull Request - State: closed - Opened by cokelaer about 2 years ago - 1 comment
Labels: enhancement

#761 - ability to have several features in rnaseq/rnadiff pipeline

Pull Request - State: closed - Opened by cokelaer about 2 years ago

#760 - add list of wrappers in the documentation

Issue - State: closed - Opened by cokelaer about 2 years ago

#759 - Ribodesigner improvements and fixes

Pull Request - State: closed - Opened by cokelaer about 2 years ago
Labels: enhancement

#758 - fix variable name img_scatter for kegg enrichment module

Pull Request - State: closed - Opened by khourhin about 2 years ago

#757 - Fix dropna warning in rnadiff get_gene_lists

Pull Request - State: closed - Opened by khourhin about 2 years ago - 1 comment

#756 - Remove the ability to use existing snpeff DB

Pull Request - State: closed - Opened by cokelaer about 2 years ago - 1 comment

#755 - Dev

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#754 - Fix incomplete annotation for kegg enrichment

Pull Request - State: closed - Opened by cokelaer over 2 years ago

#753 - Refactorize kegg enrichment module and add "all" gene list enrichment

Pull Request - State: closed - Opened by khourhin over 2 years ago

#752 - Add the save_core_genome method for buso

Pull Request - State: closed - Opened by cokelaer over 2 years ago

#751 - Add busco core genome extraction

Pull Request - State: closed - Opened by cokelaer over 2 years ago

#750 - Fixing snpeff regression

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#749 - Some updates/cleanup

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#748 - ERROR: Cannot uninstall 'ruamel-yaml'.

Issue - State: closed - Opened by Saurias92 over 2 years ago - 1 comment

#747 - add new uniprot module for GO enrichment

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#746 - implement GO enrichment using uniprot

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: New features/enhancement, 5

#745 - adapt busco parser to v5.0.0

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: bug, enhancement

#744 - new stable release

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#743 - pin click to >=8.1.0 (rnadif command accordingly)

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#742 - New conda release

Issue - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#741 - Fix requirements and cleaning tests

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#740 - Ribodesigner improved algo and vizu

Pull Request - State: closed - Opened by khourhin over 2 years ago - 1 comment

#739 - Sequanix doesn't start: SystemError during GUI initialisation

Issue - State: closed - Opened by mptrsen over 2 years ago

#738 - update metada and RTD

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#737 - update metadata

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#736 - Dev

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#735 - remove busco

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#734 - Remove busco and fix MANIFEST

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#733 - Fixing RTD by updating conda env

Pull Request - State: closed - Opened by cokelaer over 2 years ago

#732 - Update readthedocs

Pull Request - State: closed - Opened by cokelaer over 2 years ago

#731 - General cleanup (doc/test)

Pull Request - State: closed - Opened by cokelaer over 2 years ago

#730 - busco module and assembly are probably not required anymore (now in lora)

Issue - State: closed - Opened by cokelaer over 2 years ago

#729 - Fix quality_control pipeline

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: refactoring

#728 - Fix documentation

Issue - State: closed - Opened by cokelaer over 2 years ago

#727 - update version

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#726 - Dev

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#725 - Fix bug when samples names are provide

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#724 - update doc

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#723 - Fix visualisation and cleanup lane_merging

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#722 - remove useless rules, and update multitax plot

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#721 - Fix kraken empty file

Pull Request - State: closed - Opened by cokelaer over 2 years ago - 1 comment

#720 - split main script

Pull Request - State: closed - Opened by ddesvillechabrol over 2 years ago

#718 - rnaseq ribosomal detection error with bowtie on mm10

Issue - State: closed - Opened by cokelaer over 2 years ago - 1 comment
Labels: bug

#716 - separate the main 'sequana' script into submodules

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: enhancement

#714 - Update documentation

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: Todo, 1

#707 - bug in genbank parser

Issue - State: closed - Opened by cokelaer almost 3 years ago - 1 comment
Labels: bug

#704 - Optimise fasta

Pull Request - State: closed - Opened by cokelaer almost 3 years ago - 1 comment

#701 - remove some rules and fix an import

Pull Request - State: closed - Opened by cokelaer almost 3 years ago - 1 comment

#695 - refactorisation to use vcfpy instead of pyVCF

Pull Request - State: closed - Opened by cokelaer almost 3 years ago - 2 comments

#693 - Update sequana recipe on bioconda

Issue - State: closed - Opened by cokelaer almost 3 years ago - 2 comments
Labels: enhancement

#681 - scripts bam_splitter can be removed

Issue - State: closed - Opened by cokelaer about 3 years ago - 1 comment
Labels: enhancement

#677 - Some cleanup not including in previous PR

Pull Request - State: closed - Opened by cokelaer about 3 years ago

#661 - Enrichment

Pull Request - State: closed - Opened by cokelaer about 3 years ago

#660 - add more doc for pipeline development

Issue - State: closed - Opened by cokelaer about 3 years ago
Labels: documentation

#651 - remove snaketools and pipeline_common

Pull Request - State: closed - Opened by ddesvillechabrol about 3 years ago

#645 - Remove sequanix

Pull Request - State: closed - Opened by ddesvillechabrol about 3 years ago

#632 - Remove duplicate info in multiqc/reports.

Issue - State: closed - Opened by khourhin about 3 years ago - 1 comment
Labels: enhancement

#631 - sequana pipeline manager naming sample wrongly

Issue - State: closed - Opened by cokelaer about 3 years ago - 1 comment
Labels: bug

#620 - restructuration of modules into sub-directories

Issue - State: closed - Opened by cokelaer about 3 years ago - 1 comment
Labels: refactoring

#611 - rnadiff command improvments

Pull Request - State: closed - Opened by cokelaer over 3 years ago - 2 comments

#566 - This chromosome is large. Plots in the HTML reports are skipped

Issue - State: closed - Opened by Lutri22 over 5 years ago - 1 comment

#496 - Implement "subtraction" wrapper

Issue - State: closed - Opened by cokelaer over 6 years ago - 1 comment
Labels: New features/enhancement

GitHub / sequana/sequana issues and pull requests