Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / sequana/sequana issues and pull requests
#860 - Easier reruns for panther enrichment
Pull Request -
State: closed - Opened by khourhin about 1 month ago
- 1 comment
#859 - Update rnadiff (handling of batch effects, plots)
Pull Request -
State: closed - Opened by cokelaer about 2 months ago
- 1 comment
#858 - Fix dependencies; add tests
Pull Request -
State: closed - Opened by cokelaer about 2 months ago
- 1 comment
#857 - Slight update regarding iem module
Pull Request -
State: closed - Opened by cokelaer 2 months ago
- 1 comment
#856 - Major update
Pull Request -
State: closed - Opened by cokelaer 2 months ago
- 1 comment
#855 - in rnadiff, batch effect column must be named batch for now. need something generic
Issue -
State: closed - Opened by cokelaer 4 months ago
Labels: bug, New features/enhancement
#854 - transform batch into string
Issue -
State: closed - Opened by cokelaer 5 months ago
Labels: bug
#853 - Update taxonomy so as to retrieve DBs from zenodo (toydb and viruses)
Pull Request -
State: closed - Opened by cokelaer 7 months ago
- 1 comment
#852 - Various update includes rnadiff HTML fix
Pull Request -
State: closed - Opened by cokelaer 7 months ago
- 1 comment
#851 - Refactorise VCF_freebayes class and other simplification
Pull Request -
State: closed - Opened by cokelaer 7 months ago
- 1 comment
#850 - remove vcf_filter and move filters in freebayes_vcf_filter
Issue -
State: closed - Opened by cokelaer 7 months ago
#849 - refactor VCF code
Pull Request -
State: closed - Opened by cokelaer 7 months ago
#848 - Fix pyproject readme key (must be set to README; extra licence is incorrect)
Issue -
State: closed - Opened by cokelaer 7 months ago
#847 - Revisit taxonomy module to save data in csv.gz
Pull Request -
State: closed - Opened by cokelaer 7 months ago
- 1 comment
#846 - Major update of PCA computation + batch effect figures
Pull Request -
State: closed - Opened by cokelaer 8 months ago
- 1 comment
#845 - Include corrected PCA inside rnadiff module
Issue -
State: open - Opened by cokelaer 8 months ago
- 1 comment
Labels: enhancement
#844 - Include arbitrary model in sequana differential analysis
Issue -
State: closed - Opened by cokelaer 8 months ago
#843 - Minor doc addition for kegg enrichment report
Pull Request -
State: closed - Opened by khourhin 8 months ago
- 1 comment
#842 - Update ribodesigner methods / more checls for IEM and rnadiff design
Pull Request -
State: closed - Opened by cokelaer 8 months ago
#841 - Fix example and update metadata
Pull Request -
State: closed - Opened by cokelaer 8 months ago
#840 - cleanup and fix doc error
Pull Request -
State: closed - Opened by cokelaer 8 months ago
- 1 comment
#839 - Update IEM
Pull Request -
State: closed - Opened by cokelaer 8 months ago
- 1 comment
#838 - optimise variant parser in freebayes_vcf
Issue -
State: closed - Opened by cokelaer 8 months ago
- 1 comment
Labels: enhancement
#837 - Can use RNAdiff without GFF file, so removing click "required"
Pull Request -
State: closed - Opened by khourhin 9 months ago
- 1 comment
#836 - Fix CI for pypi
Pull Request -
State: closed - Opened by cokelaer 9 months ago
- 1 comment
#835 - Switch to pyproject
Pull Request -
State: closed - Opened by cokelaer 9 months ago
- 2 comments
#834 - Hotfixes
Pull Request -
State: closed - Opened by cokelaer 10 months ago
#833 - volcano plot xlim should ignore gene with null pvalue
Issue -
State: closed - Opened by cokelaer 10 months ago
- 1 comment
#832 - Update RTD
Pull Request -
State: closed - Opened by cokelaer 10 months ago
- 1 comment
#831 - Fix wrong import
Pull Request -
State: closed - Opened by cokelaer 10 months ago
- 1 comment
#830 - Fix taxonomy to accept several databases (regression)
Pull Request -
State: closed - Opened by cokelaer 10 months ago
- 1 comment
#829 - add missing script for g4hunter
Pull Request -
State: closed - Opened by cokelaer 11 months ago
- 1 comment
#828 - add g4hunter, fix kegg
Pull Request -
State: closed - Opened by cokelaer 11 months ago
- 1 comment
#827 - Save kegg pathways in /config/sequana in sequana enrichment_kegg standalone
Issue -
State: closed - Opened by cokelaer 11 months ago
- 1 comment
#827 - Save kegg pathways in /config/sequana in sequana enrichment_kegg standalone
Issue -
State: open - Opened by cokelaer 11 months ago
#826 - warning deprecated
Issue -
State: closed - Opened by cokelaer 11 months ago
#825 - Major refactoring sequana_coverage
Pull Request -
State: closed - Opened by cokelaer 11 months ago
- 1 comment
#824 - New seaborn syntax breaks the rnadiff.plot_normalisation
Issue -
State: closed - Opened by cokelaer 12 months ago
- 1 comment
#823 - Update for chipseq pipeline, sequana_coverage update to handle small eukaryotes
Pull Request -
State: closed - Opened by cokelaer 12 months ago
- 1 comment
#823 - Update for chipseq pipeline, sequana_coverage update to handle small eukaryotes
Pull Request -
State: closed - Opened by cokelaer 12 months ago
- 1 comment
#822 - Implement mpileup module
Pull Request -
State: closed - Opened by cokelaer 12 months ago
- 1 comment
#821 - Homogenize enrichments clis and fix pb when no DEGs in panther
Pull Request -
State: closed - Opened by khourhin 12 months ago
- 1 comment
#820 - Cleanup and fix annotation in rnadiff.py
Pull Request -
State: closed - Opened by cokelaer 12 months ago
- 1 comment
#819 - Implement new figure in the RNAseq pipeline
Pull Request -
State: closed - Opened by cokelaer about 1 year ago
- 1 comment
#818 - Fix rnadiff annotation and kegg pathways download/reuse
Pull Request -
State: closed - Opened by khourhin about 1 year ago
- 1 comment
#817 - minor simplification
Pull Request -
State: closed - Opened by khourhin about 1 year ago
#816 - add version within reports. More plotly plots
Pull Request -
State: closed - Opened by cokelaer about 1 year ago
- 1 comment
#815 - Remove keep_conditions option from sequana rnadiff
Issue -
State: closed - Opened by cokelaer about 1 year ago
- 1 comment
#814 - Fixing KEGG colored pathway
Pull Request -
State: closed - Opened by cokelaer about 1 year ago
- 1 comment
#813 - add new plot for the sequana_mapper pipeline and others
Pull Request -
State: closed - Opened by cokelaer about 1 year ago
#812 - sequana enrichment-kegg imporvements
Issue -
State: closed - Opened by cokelaer about 1 year ago
#811 - Enrichment report fix and improvements
Pull Request -
State: closed - Opened by khourhin about 1 year ago
- 1 comment
#810 - update compare/iem/rnadiff modules
Pull Request -
State: closed - Opened by cokelaer about 1 year ago
- 1 comment
#809 - Fix overlapping labels and wrong axis in kegg scatterplot
Pull Request -
State: closed - Opened by khourhin over 1 year ago
- 1 comment
#808 - Update ribodesigner
Pull Request -
State: closed - Opened by cokelaer over 1 year ago
- 1 comment
#807 - Adding table export as csv for kegg and GO enrichment
Pull Request -
State: closed - Opened by khourhin over 1 year ago
- 1 comment
#806 - Fix RTD and update version
Pull Request -
State: closed - Opened by cokelaer over 1 year ago
- 1 comment
#805 - fix images directory for modules, and gff improvments
Pull Request -
State: closed - Opened by cokelaer over 1 year ago
- 1 comment
#804 - GFF3 does not handle FASTA field
Issue -
State: closed - Opened by ddesvillechabrol over 1 year ago
#803 - GFF3 take into account special character
Issue -
State: closed - Opened by cokelaer over 1 year ago
#802 - Update IEM module to check samplesheet
Pull Request -
State: closed - Opened by cokelaer over 1 year ago
- 2 comments
#801 - fix missing information
Pull Request -
State: closed - Opened by ddesvillechabrol over 1 year ago
- 1 comment
#800 - Fix #780 and rename gtf into gtf_fixer
Pull Request -
State: closed - Opened by cokelaer over 1 year ago
- 1 comment
#799 - Update ribodesigner
Pull Request -
State: closed - Opened by cokelaer over 1 year ago
- 2 comments
#798 - add sequana variants_comparison
Pull Request -
State: closed - Opened by ddesvillechabrol over 1 year ago
- 1 comment
#797 - add gff annotation for sequana_coverage
Pull Request -
State: closed - Opened by ddesvillechabrol over 1 year ago
- 1 comment
#796 - Update rnadiff command and reports
Pull Request -
State: closed - Opened by cokelaer over 1 year ago
- 1 comment
#795 - sequana coverage could export a track (bed) for IGV
Issue -
State: open - Opened by cokelaer over 1 year ago
#794 - Fix the apptainers in current pipelines tht are failing on CI action
Issue -
State: closed - Opened by cokelaer over 1 year ago
Labels: bug
#793 - update CI to use correct mamba
Pull Request -
State: closed - Opened by cokelaer over 1 year ago
- 1 comment
#792 - Ribodesigner: verify the rRNA annotations
Issue -
State: open - Opened by khourhin over 1 year ago
#791 - Fix metadata and remove useless rules
Pull Request -
State: closed - Opened by cokelaer over 1 year ago
- 1 comment
#790 - Fix test due to bioservices updates
Pull Request -
State: closed - Opened by cokelaer almost 2 years ago
- 1 comment
#789 - merge dev branch into main before release
Pull Request -
State: closed - Opened by cokelaer almost 2 years ago
- 1 comment
#788 - handle the future warnings
Issue -
State: closed - Opened by cokelaer almost 2 years ago
- 1 comment
#787 - Adding shrinked LFC to rnadiff dataframe as default LFC values
Pull Request -
State: closed - Opened by khourhin almost 2 years ago
- 2 comments
#786 - Add new modules in relation with chipseq pipelines
Pull Request -
State: closed - Opened by cokelaer almost 2 years ago
- 1 comment
#785 - Chipseq modules
Pull Request -
State: closed - Opened by cokelaer almost 2 years ago
#784 - Use gff as annotation in the sequana_coverage tool
Issue -
State: closed - Opened by cokelaer almost 2 years ago
Labels: 3, enhancement
#783 - add fasta_and_gff_correction and codon modules
Pull Request -
State: closed - Opened by cokelaer almost 2 years ago
- 1 comment
#782 - code to correct fasta and gff given a VCF file
Issue -
State: closed - Opened by cokelaer almost 2 years ago
Labels: 3
#781 - sequana coverage would benefit from an annotation in the html report
Issue -
State: closed - Opened by cokelaer almost 2 years ago
- 1 comment
#780 - gtf-fixer sub command improvements
Issue -
State: closed - Opened by cokelaer almost 2 years ago
- 1 comment
#779 - GFF3 create_files_for_rnadif can be removed
Issue -
State: closed - Opened by cokelaer almost 2 years ago
- 1 comment
#778 - add snpeff build options
Pull Request -
State: closed - Opened by cokelaer almost 2 years ago
#777 - force chrom name as string in bedtools
Pull Request -
State: closed - Opened by ddesvillechabrol almost 2 years ago
#776 - sequana_coverage bug if name is just a number
Issue -
State: closed - Opened by ddesvillechabrol almost 2 years ago
#775 - Fix export bug when not clustering, adding gff filtered export
Pull Request -
State: closed - Opened by khourhin almost 2 years ago
- 2 comments
#774 - Fix falco and update requirements
Pull Request -
State: closed - Opened by cokelaer almost 2 years ago
- 1 comment
#773 - fix typo
Pull Request -
State: closed - Opened by cokelaer almost 2 years ago
#772 - Fixing condition column name selection when filtering by mean by groups
Pull Request -
State: closed - Opened by khourhin almost 2 years ago
#771 - hotfix on kegg pathway to add back the up DGE
Pull Request -
State: closed - Opened by cokelaer almost 2 years ago
#770 - KEGG pathways seem to be missing the up regulated in annotated image
Issue -
State: closed - Opened by cokelaer almost 2 years ago
#769 - KEGG pathways seem to be downloaded twice
Issue -
State: closed - Opened by cokelaer almost 2 years ago
Labels: 1, enhancement
#768 - Update kegg/panther to handle special cases
Pull Request -
State: closed - Opened by cokelaer about 2 years ago
#767 - rename master into main
Pull Request -
State: closed - Opened by cokelaer about 2 years ago
- 1 comment
#766 - Merge pull request #765 from sequana/main
Pull Request -
State: closed - Opened by cokelaer about 2 years ago
#765 - merge main into dev
Pull Request -
State: closed - Opened by cokelaer about 2 years ago
- 1 comment
#764 - merge main into dev
Pull Request -
State: closed - Opened by cokelaer about 2 years ago
#763 - Update rnadiff to use several features; add fisher for variant calling; pinning requirements
Pull Request -
State: closed - Opened by cokelaer about 2 years ago