Ecosyste.ms: Issues

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GitHub / sequana/sequana issues and pull requests

#855 - in rnadiff, batch effect column must be named batch for now. need something generic

Issue - State: open - Opened by cokelaer about 1 month ago
Labels: bug, New features/enhancement

#854 - transform batch into string

Issue - State: open - Opened by cokelaer 2 months ago
Labels: bug

#853 - Update taxonomy so as to retrieve DBs from zenodo (toydb and viruses)

Pull Request - State: closed - Opened by cokelaer 4 months ago - 1 comment

#852 - Various update includes rnadiff HTML fix

Pull Request - State: closed - Opened by cokelaer 4 months ago - 1 comment

#851 - Refactorise VCF_freebayes class and other simplification

Pull Request - State: closed - Opened by cokelaer 4 months ago - 1 comment

#849 - refactor VCF code

Pull Request - State: closed - Opened by cokelaer 4 months ago

#847 - Revisit taxonomy module to save data in csv.gz

Pull Request - State: closed - Opened by cokelaer 4 months ago - 1 comment

#846 - Major update of PCA computation + batch effect figures

Pull Request - State: closed - Opened by cokelaer 5 months ago - 1 comment

#845 - Include corrected PCA inside rnadiff module

Issue - State: open - Opened by cokelaer 5 months ago - 1 comment

#843 - Minor doc addition for kegg enrichment report

Pull Request - State: closed - Opened by khourhin 5 months ago - 1 comment

#841 - Fix example and update metadata

Pull Request - State: closed - Opened by cokelaer 5 months ago

#840 - cleanup and fix doc error

Pull Request - State: closed - Opened by cokelaer 5 months ago - 1 comment

#839 - Update IEM

Pull Request - State: closed - Opened by cokelaer 5 months ago - 1 comment

#838 - optimise variant parser in freebayes_vcf

Issue - State: closed - Opened by cokelaer 5 months ago - 1 comment
Labels: enhancement

#837 - Can use RNAdiff without GFF file, so removing click "required"

Pull Request - State: closed - Opened by khourhin 6 months ago - 1 comment

#836 - Fix CI for pypi

Pull Request - State: closed - Opened by cokelaer 6 months ago - 1 comment

#835 - Switch to pyproject

Pull Request - State: closed - Opened by cokelaer 6 months ago - 2 comments

#834 - Hotfixes

Pull Request - State: closed - Opened by cokelaer 7 months ago

#833 - volcano plot xlim should ignore gene with null pvalue

Issue - State: closed - Opened by cokelaer 7 months ago - 1 comment

#832 - Update RTD

Pull Request - State: closed - Opened by cokelaer 7 months ago - 1 comment

#831 - Fix wrong import

Pull Request - State: closed - Opened by cokelaer 7 months ago - 1 comment

#830 - Fix taxonomy to accept several databases (regression)

Pull Request - State: closed - Opened by cokelaer 7 months ago - 1 comment

#829 - add missing script for g4hunter

Pull Request - State: closed - Opened by cokelaer 8 months ago - 1 comment

#828 - add g4hunter, fix kegg

Pull Request - State: closed - Opened by cokelaer 8 months ago - 1 comment

#826 - warning deprecated

Issue - State: closed - Opened by cokelaer 8 months ago

#825 - Major refactoring sequana_coverage

Pull Request - State: closed - Opened by cokelaer 8 months ago - 1 comment

#824 - New seaborn syntax breaks the rnadiff.plot_normalisation

Issue - State: closed - Opened by cokelaer 9 months ago - 1 comment

#823 - Update for chipseq pipeline, sequana_coverage update to handle small eukaryotes

Pull Request - State: closed - Opened by cokelaer 9 months ago - 1 comment

#823 - Update for chipseq pipeline, sequana_coverage update to handle small eukaryotes

Pull Request - State: closed - Opened by cokelaer 9 months ago - 1 comment

#822 - Implement mpileup module

Pull Request - State: closed - Opened by cokelaer 9 months ago - 1 comment

#821 - Homogenize enrichments clis and fix pb when no DEGs in panther

Pull Request - State: closed - Opened by khourhin 9 months ago - 1 comment

#820 - Cleanup and fix annotation in rnadiff.py

Pull Request - State: closed - Opened by cokelaer 9 months ago - 1 comment

#819 - Implement new figure in the RNAseq pipeline

Pull Request - State: closed - Opened by cokelaer 9 months ago - 1 comment

#818 - Fix rnadiff annotation and kegg pathways download/reuse

Pull Request - State: closed - Opened by khourhin 9 months ago - 1 comment

#817 - minor simplification

Pull Request - State: closed - Opened by khourhin 9 months ago

#816 - add version within reports. More plotly plots

Pull Request - State: closed - Opened by cokelaer 10 months ago - 1 comment

#815 - Remove keep_conditions option from sequana rnadiff

Issue - State: closed - Opened by cokelaer 10 months ago - 1 comment

#814 - Fixing KEGG colored pathway

Pull Request - State: closed - Opened by cokelaer 10 months ago - 1 comment

#813 - add new plot for the sequana_mapper pipeline and others

Pull Request - State: closed - Opened by cokelaer 10 months ago

#812 - sequana enrichment-kegg imporvements

Issue - State: closed - Opened by cokelaer 11 months ago

#811 - Enrichment report fix and improvements

Pull Request - State: closed - Opened by khourhin 12 months ago - 1 comment

#810 - update compare/iem/rnadiff modules

Pull Request - State: closed - Opened by cokelaer 12 months ago - 1 comment

#809 - Fix overlapping labels and wrong axis in kegg scatterplot

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

#808 - Update ribodesigner

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

#807 - Adding table export as csv for kegg and GO enrichment

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

#806 - Fix RTD and update version

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

#805 - fix images directory for modules, and gff improvments

Pull Request - State: closed - Opened by cokelaer about 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 over 1 year ago - 1 comment

#789 - merge dev branch into main before release

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

#788 - handle the future warnings

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

#787 - Adding shrinked LFC to rnadiff dataframe as default LFC values

Pull Request - State: closed - Opened by khourhin over 1 year ago - 2 comments

#786 - Add new modules in relation with chipseq pipelines

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

#785 - Chipseq modules

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#784 - Use gff as annotation in the sequana_coverage tool

Issue - State: closed - Opened by cokelaer over 1 year ago
Labels: 3, enhancement

#783 - add fasta_and_gff_correction and codon modules

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

#782 - code to correct fasta and gff given a VCF file

Issue - State: closed - Opened by cokelaer over 1 year ago
Labels: 3

#781 - sequana coverage would benefit from an annotation in the html report

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

#780 - gtf-fixer sub command improvements

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

#779 - GFF3 create_files_for_rnadif can be removed

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

#778 - add snpeff build options

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#777 - force chrom name as string in bedtools

Pull Request - State: closed - Opened by ddesvillechabrol over 1 year ago

#776 - sequana_coverage bug if name is just a number

Issue - State: closed - Opened by ddesvillechabrol over 1 year ago

#775 - Fix export bug when not clustering, adding gff filtered export

Pull Request - State: closed - Opened by khourhin over 1 year ago - 2 comments

#774 - Fix falco and update requirements

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

#773 - fix typo

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#771 - hotfix on kegg pathway to add back the up DGE

Pull Request - State: closed - Opened by cokelaer over 1 year ago

#769 - KEGG pathways seem to be downloaded twice

Issue - State: closed - Opened by cokelaer over 1 year ago
Labels: 1, enhancement

#768 - Update kegg/panther to handle special cases

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

#767 - rename master into main

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

#766 - Merge pull request #765 from sequana/main

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

#765 - merge main into dev

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

#764 - merge main into dev

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

#762 - add fisher test in variant calling

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

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

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

#760 - add list of wrappers in the documentation

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

#759 - Ribodesigner improvements and fixes

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

#758 - fix variable name img_scatter for kegg enrichment module

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