Releases | Open Source Science

What's Changed

New set of modules and improvements by @cokelaer in https://github.com/sequana/sequana/pull/868

Full Changelog: https://github.com/sequana/sequana/compare/v0.19.1...v0.19.2

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer 5 months ago

What's Changed

Modify path to find the images downloaded from KEGG by chromedriver by @khourhin in https://github.com/sequana/sequana/pull/865
various update including variant plots by @cokelaer in https://github.com/sequana/sequana/pull/866
update pyproject dependencies

Full Changelog: https://github.com/sequana/sequana/compare/v0.19.0...v0.19.1

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer 10 months ago

What's Changed

Easier reruns for panther enrichment by @khourhin in https://github.com/sequana/sequana/pull/860
add somy, improved coverage by @cokelaer in https://github.com/sequana/sequana/pull/861

Full Changelog: https://github.com/sequana/sequana/compare/v0.17.3...v0.19.0

What's Changed

Major update with new modules and pyproject deprecation fixes by @cokelaer in https://github.com/sequana/sequana/pull/863
drop support for python 3.8
NEW modules: kozak, somy score, telomere, biomol, rnafold, restriction enzyme
UPDATES: sequence module has more metrics (e.g. karlin signature), fastq has a histogram for long reads, drop matplotlib-venn dependencies in favor of pure sequana.viz.venn module

Full Changelog: https://github.com/sequana/sequana/compare/v0.18.0...v0.19.0

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer 11 months ago

What's Changed

Easier reruns for panther enrichment by @khourhin in https://github.com/sequana/sequana/pull/860
add somy, improved coverage by @cokelaer in https://github.com/sequana/sequana/pull/861

Full Changelog: https://github.com/sequana/sequana/compare/v0.17.3...v0.18.0

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 1 year ago

What's Changed

Update rnadiff (handling of batch effects, plots) by @cokelaer in https://github.com/sequana/sequana/pull/859

Full Changelog: https://github.com/sequana/sequana/compare/v0.17.2...v0.17.3

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer over 1 year ago

What's Changed

Fix dependencies to be useful for all pipelines; add tests by @cokelaer in https://github.com/sequana/sequana/pull/858

Full Changelog: https://github.com/sequana/sequana/compare/v0.17.1...v0.17.2

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer over 1 year ago

What's Changed

Slight update regarding iem module by @cokelaer in https://github.com/sequana/sequana/pull/857

Full Changelog: https://github.com/sequana/sequana/compare/v0.17.0...v0.17.1

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer over 1 year ago

What's Changed

Major update by @cokelaer in https://github.com/sequana/sequana/pull/856

Full Changelog: https://github.com/sequana/sequana/compare/v0.16.11...v0.17.0

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer over 1 year ago

What's Changed

Various update includes rnadiff HTML fix by @cokelaer in https://github.com/sequana/sequana/pull/852
Update taxonomy so as to retrieve DBs from zenodo (toydb and viruses) by @cokelaer in https://github.com/sequana/sequana/pull/853

Full Changelog: https://github.com/sequana/sequana/compare/v0.16.10...v0.16.11

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 2 years ago

What's Changed

Refactorise VCF_freebayes class and other simplification by @cokelaer in https://github.com/sequana/sequana/pull/851

Full Changelog: https://github.com/sequana/sequana/compare/v0.16.9...v0.16.10

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 2 years ago

What's Changed

Major update of PCA computation + batch effect figures by @cokelaer in https://github.com/sequana/sequana/pull/846
Revisit taxonomy module to save data in csv.gz by @cokelaer in https://github.com/sequana/sequana/pull/847

Full Changelog: https://github.com/sequana/sequana/compare/v0.16.8...v0.16.9

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 2 years ago

What's Changed

Update ribodesigner methods / more checls for IEM and rnadiff design by @cokelaer in https://github.com/sequana/sequana/pull/842
Minor doc addition for kegg enrichment report by @khourhin in https://github.com/sequana/sequana/pull/843

Full Changelog: https://github.com/sequana/sequana/compare/v0.16.7...v0.16.8

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 2 years ago

What's Changed

cleanup and fix doc error by @cokelaer in https://github.com/sequana/sequana/pull/840
Fix example and update metadata by @cokelaer in https://github.com/sequana/sequana/pull/841

Full Changelog: https://github.com/sequana/sequana/compare/v0.16.6...v0.16.7

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 2 years ago

What's Changed

Can use RNAdiff without GFF file, so removing click "required" by @khourhin in https://github.com/sequana/sequana/pull/837
Update IEM by @cokelaer in https://github.com/sequana/sequana/pull/839

Full Changelog: https://github.com/sequana/sequana/compare/v0.16.5...v0.16.6

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 2 years ago

What's Changed

Switch to pyproject by @cokelaer in https://github.com/sequana/sequana/pull/835
Fix CI for pypi by @cokelaer in https://github.com/sequana/sequana/pull/836

Full Changelog: https://github.com/sequana/sequana/compare/v0.16.4...v0.16.5

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 2 years ago

What's Changed

Update RTD by @cokelaer in https://github.com/sequana/sequana/pull/832
Hotfixes by @cokelaer in https://github.com/sequana/sequana/pull/834

Full Changelog: https://github.com/sequana/sequana/compare/v0.16.3...v0.16.4

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 2 years ago

What's Changed

Fix taxonomy to accept several databases (regression) by @cokelaer in https://github.com/sequana/sequana/pull/830
Fix wrong import by @cokelaer in https://github.com/sequana/sequana/pull/831

Full Changelog: https://github.com/sequana/sequana/compare/v0.16.1...v0.16.3

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 2 years ago

What's Changed

add missing script for g4hunter by @cokelaer in https://github.com/sequana/sequana/pull/829
fix regression in coverage and taxonomy

Full Changelog: https://github.com/sequana/sequana/compare/v0.16.0...v0.16.2

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 2 years ago

'Sequana' - v0.16.1

hotfix missing module

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 2 years ago

What's Changed

Cleanup and fix annotation in rnadiff.py by @cokelaer in https://github.com/sequana/sequana/pull/820
Homogenize enrichments clis and fix pb when no DEGs in panther by @khourhin in https://github.com/sequana/sequana/pull/821
Implement mpileup module by @cokelaer in https://github.com/sequana/sequana/pull/822
Update for chipseq pipeline, sequana_coverage update to handle small eukaryotes by @cokelaer in https://github.com/sequana/sequana/pull/823
Major refactoring sequana_coverage by @cokelaer in https://github.com/sequana/sequana/pull/825
add g4hunter, fix kegg by @cokelaer in https://github.com/sequana/sequana/pull/828

Full Changelog: https://github.com/sequana/sequana/compare/v0.15.4...v0.16.0

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 2 years ago

What's Changed

minor simplification by @khourhin in https://github.com/sequana/sequana/pull/817
Fix rnadiff annotation and kegg pathways download/reuse by @khourhin in https://github.com/sequana/sequana/pull/818
Implement new figure in the RNAseq pipeline by @cokelaer in https://github.com/sequana/sequana/pull/819

Full Changelog: https://github.com/sequana/sequana/compare/v0.15.3...v0.15.4

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 2 years ago

What's Changed

Enrichment report fix and improvements by @khourhin in https://github.com/sequana/sequana/pull/811
add new plot for the sequana_mapper pipeline and others by @cokelaer in https://github.com/sequana/sequana/pull/813
Fixing KEGG colored pathway by @cokelaer in https://github.com/sequana/sequana/pull/814
add version within reports. More plotly plots by @cokelaer in https://github.com/sequana/sequana/pull/816

Full Changelog: https://github.com/sequana/sequana/compare/v0.15.2...v0.15.3

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer over 2 years ago

What's Changed

Adding table export as csv for kegg and GO enrichment by @khourhin in https://github.com/sequana/sequana/pull/807
Update ribodesigner by @cokelaer in https://github.com/sequana/sequana/pull/808
update compare/iem/rnadiff modules by @cokelaer in https://github.com/sequana/sequana/pull/810

Full Changelog: https://github.com/sequana/sequana/compare/v0.15.1...v0.15.2

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer over 2 years ago

What's Changed

fix images directory for modules, and gff improvments by @cokelaer in https://github.com/sequana/sequana/pull/805
Fix RTD and update version by @cokelaer in https://github.com/sequana/sequana/pull/806

Full Changelog: https://github.com/sequana/sequana/compare/v0.15.0...v0.15.1

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer over 2 years ago

What's Changed

Add new modules in relation with chipseq pipelines by @cokelaer in https://github.com/sequana/sequana/pull/786
Fix test due to bioservices updates by @cokelaer in https://github.com/sequana/sequana/pull/790
remove useless rules by @cokelaer in https://github.com/sequana/sequana/pull/791
update CI to use correct mamba by @cokelaer in https://github.com/sequana/sequana/pull/793
Adding shrinked LFC to rnadiff dataframe as default LFC values by @khourhin in https://github.com/sequana/sequana/pull/787
Update rnadiff command and reports by @cokelaer in https://github.com/sequana/sequana/pull/796
add gff annotation for sequana_coverage by @ddesvillechabrol in https://github.com/sequana/sequana/pull/797
add sequana variants_comparison by @ddesvillechabrol in https://github.com/sequana/sequana/pull/798
Update ribodesigner by @cokelaer in https://github.com/sequana/sequana/pull/799
Fix #780 and rename gtf into gtf_fixer by @cokelaer in https://github.com/sequana/sequana/pull/800
fix missing information by @ddesvillechabrol in https://github.com/sequana/sequana/pull/801
Update IEM module to check samplesheet by @cokelaer in https://github.com/sequana/sequana/pull/802

Full Changelog: https://github.com/sequana/sequana/compare/v0.14.6...v0.15.0

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer over 2 years ago

What's Changed

add fastaandgff_correction and codon modules by @cokelaer in https://github.com/sequana/sequana/pull/783
add modules for ChIP-seq analysis

Full Changelog: https://github.com/sequana/sequana/compare/v0.14.5...v0.14.6

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 3 years ago

What's Changed

Fixing condition column name selection when filtering by mean by groups by @khourhin in https://github.com/sequana/sequana/pull/772
Fix export bug when not clustering, adding gff filtered export by @khourhin in https://github.com/sequana/sequana/pull/775
force chrom name as string in bedtools by @ddesvillechabrol in https://github.com/sequana/sequana/pull/777
add snpeff build options by @cokelaer in https://github.com/sequana/sequana/pull/778

Full Changelog: https://github.com/sequana/sequana/compare/v0.14.4...v0.14.5

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 3 years ago

What's Changed

Update kegg/panther to handle special cases by @cokelaer in https://github.com/sequana/sequana/pull/768
hotfix on kegg pathway to add back the up DGE by @cokelaer in https://github.com/sequana/sequana/pull/771
Fix falco in fastqc by @cokelaer in https://github.com/sequana/sequana/pull/774
remove pin on cookicutter and requires snakemake >=7.16

Full Changelog: https://github.com/sequana/sequana/compare/v0.14.3...v0.14.4

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 3 years ago

What's Changed

ability to have several features in rnaseq/rnadiff pipeline by @cokelaer in https://github.com/sequana/sequana/pull/761
add fisher test in variant calling by @cokelaer in https://github.com/sequana/sequana/pull/762
Update rnadiff to use several features
add fisher for variant calling
pinning requirements by @cokelaer in https://github.com/sequana/sequana/pull/763
rename master into main by @cokelaer in https://github.com/sequana/sequana/pull/767

Full Changelog: https://github.com/sequana/sequana/compare/v0.14.2...v0.14.3

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer over 3 years ago

What's Changed

Remove the ability to use existing snpeff DB by @cokelaer in https://github.com/sequana/sequana/pull/756
Fix dropna warning in rnadiff getgenelists by @khourhin in https://github.com/sequana/sequana/pull/757
fix variable name img_scatter for kegg enrichment module by @khourhin in https://github.com/sequana/sequana/pull/758
Ribodesigner improvements and fixes by @cokelaer in https://github.com/sequana/sequana/pull/759

Full Changelog: https://github.com/sequana/sequana/compare/v0.14.1...v0.14.2

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer over 3 years ago

'Sequana' - v0.14.1

Release with uniprot enrichment and various improvements to increase robustness of enrichments.

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer over 3 years ago

'Sequana' - v0.14.0

Release for bioconda with ribodesigner included

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 4 years ago

'Sequana' - v0.13.2

Stable Release with new way to install official pipelines

pip install sequana[pipelines]

Also 0.13.2 is a lighter version with 5Mb instead of 16Mb

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 4 years ago

'Sequana' - v0.13.1

hotfix fixing MANIFEST and remove busco module now in Lora pipeline

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 4 years ago

'Sequana' - v0.13.0

restructuration main command
add ribodesigner tool

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 4 years ago

'Sequana' - v0.12.7

added ribodesigner

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer almost 4 years ago

'Sequana' - v0.12.6

Some improvements on rnaseq-related function and general cleanup

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 4 years ago

'Sequana' - v0.12.5

uses vcfpy instead of pyvcf

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 4 years ago

'Sequana' - v0.12.4

Update some sequana rules to use the new wrappers

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by cokelaer about 4 years ago