Tags: gagneurlab/drop
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DROP Release 1.6.0 The new release 1.6.0 includes: * Reorder SE object and fix gene_seqnames assignment * Add threading and memory resource management to allelicCounts * Fix MAE by removing unneeded seqlevel conversions (#661) * Enforce stringent boolean conversion from sample sheet (#657) * DNA-RNA matching conf int. (#659) * Full test script using Kremer et al data (#663) * use correct ID for MAE test (#664)
New release DROP 1.5.0 (#616) * create exception for plot best encoding dim * read in external hpo_file correctly from snakemake params * Check BAM existence for non-external groups only * fix pandas warning in SampleParams * check strand specificity in each drop group as opposed to all samples * fix build badge status * add .readthedocs.yaml v2 config file * Update .readthedocs.yaml * install sphinx_rtd_theme in .readthedocs.yaml * remomve reduntant fail_on_warning in .readthedocs.yaml * fix minor bugs in sex prediction * Update Summary.R * migrate to mamba-org/setup-micromamba in GHA * specify environment.yml in GHA * add sample annotation docs * set FRASER2 as default FRASER version * show mismatch sex dataframe only when there is a mismatch * print mismatch table instead of showing using DT * set non-external samples' GENE_ANNOTATION to null if provided * Update README.md * Update create_matrix_dna_rna_cor.R sort matrix by the sample annotation * remove space * Update README.md * added which param to vcf in dna-rna matching * prunning fixed * boxplot added * change MAE res to txt file * change MAE res to txt file * Rds to txt MAE results * fix chr and factor issue in chr * fix Rds txt file name * move libs up * Update Summary.R * Update README.md * Update README.md * Integrate Optimal Hard Threshold to find best hidden dimension (#615) * integrate OHT as default to find q in aberrant expression * change OUTRIDER source to OHT branch * add OHT key to AE test config * update requirements to use newest OUTRIDER-OHT branch * fix print message * add useOHTtoObtainQ: true to config relative * add metadata(ods)[["useOHTtoObtainQ"]] <- FALSE * add isTRUE() in if condition * add isTRUE() to if condition in Summary.R * add missing brackets in runOutrider.R * add missing brackets in Summary.R * Update prepare.rst to include useOHTtoObtainQ * add useOHTtoObtainQ in config keys for aberrant splicing * add useOHTtoObtainQ parameter in demo config for FRASER * introduce OHT in aberrant splicing * add singular value plot in summary for FRASER * add useOHTtoObtainQ parameter to test and template config * change required FRASER branch to OHT * update micromamba setup * minor changes in aberrant splicing summary * update OUTRIDER and FRASER version * fix typo error * add if statement before plotEncDimSearch in OUTRIDER summary * remove print statement for singular value plot * Revert "remove print statement for singular value plot" This reverts commit 2689159. * remove 'install' messages for testing purposes * suppress biocmanager warnings to fix dot error * Update python-package-conda.yml * Update environment.yml * update requirementsR * adjust to newest OUTRIDER version (add sinular value plot, remove findEncodingDim function) * fix missing object error * remove unused wbuild input (input_params) from OUTRIDER * minor cleanups * adapt cli to updated click package * update FRASER and OUTRIDER versions * specify exact version of OR&FR * fix gha tests * Update environment.yml * remove return from test_pipeline * Update requirementsR.txt to new FRASER version --------- Co-authored-by: Vicente Yepez <[email protected]> Co-authored-by: andrearaithel <[email protected]> Co-authored-by: Andrea Raithel <[email protected]> * Update README.md * v1.5 * Update __init__.py * Update conf.py * Update installation.rst * Update setup.cfg * Update cli.py * Update README.md * Update README.md Co-authored-by: Christian Mertes <[email protected]> * Update README.md Co-authored-by: Christian Mertes <[email protected]> * parallelize granges ods * simplify results extraction * fix mae results chr style * fix symlinking to relative path (#626) fixes #622 Co-authored-by: Vicente Yepez <[email protected]> * add license message (#628) * add license message * update contacts * Update license README * Copilot/fix 6e905f98 57a9 4ee4 a1bf e5576439cd0d (#631) * Initial plan * Enable mixed BAM and external counts for expression analysis Co-authored-by: c-mertes <[email protected]> * Add logging to inform users when external expression counts are used Co-authored-by: c-mertes <[email protected]> * fixes cases with both external and local BAM files * fixes cases with both external and local BAM files * Update python-package-conda.yml * Update python-package-conda.yml * Update installation of DT * Update requirementsR.txt * add documentation for joint bam/externalCounts input --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: c-mertes <[email protected]> Co-authored-by: Vicente <[email protected]> Co-authored-by: AtaJadidAhari <[email protected]> * make AE reproducible (#632) * computes PSI/J according to FRASER1/FRASER2 * revert psi * Small fixes (#633) * multithreading expression counting per chromosome * assign memory constrains for splicing * add export of full splicing table * run MAE counting in parallel per chromosome * fix missing inter.feature * use correct lambda function in mae_createSNV rule * Update 08_extract_results_FraseR.R --------- Co-authored-by: Vicente Yepez <[email protected]> * Update create_matrix_dna_rna_cor.R (#636) * Update create_matrix_dna_rna_cor.R * Update create_matrix_dna_rna_cor.R * Revise commercial license details for OUTRIDER and FRASER Updated licensing information for OUTRIDER and FRASER in README. * Add data.table library to Overview.R * Add data.table library to Overview.R * Update create_matrix_dna_rna_cor.R (#644) * Update requirementsR.txt (#645) * Update requirementsR.txt * add fitmetrics to AS * update tests * update AS tests * calculate splice metrics in export if needed --------- Co-authored-by: AtaJadidAhari <[email protected]> Co-authored-by: Vicente <[email protected]> Co-authored-by: andrearaithel <[email protected]> Co-authored-by: Andrea Raithel <[email protected]> Co-authored-by: Christian Mertes <[email protected]> Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: c-mertes <[email protected]>
Freeze version (#544) * fix result script in case of no significant results * fix bug merge in wrong order coverage dt * Update prepare.rst * added saving of granges of split counts .as tsv.gz * Update DNA_RNA_matrix_plot.R * change ln to softlink * add help to index * Update DNA_RNA_matrix_plot.R fix bug when multiple matching * Update create_matrix_dna_rna_cor.R Remove unnecessary step for the QC matrix * Update DNA_RNA_matrix_plot.R fix bug in not annotated QC table * Update DNA_RNA_matrix_plot.R fix bug in check matches function * Update DNA_RNA_matrix_plot.R * Update README.md * Update README.md * Update README.md * Update README.md * Update 08_extract_results_FraseR.R * Update README.md * update GHA with snakemake version range and activate PR checks * fix #532 knitr parsing * remove redundent rules to create dict and fai files * fix last outrider version install * Fix FRASER and OUTRIDER versions * OUTRIDER 1.16.2 & FRASER 1.99.0 * pin OUTRIDER to 1.20.1 * pin FRASER to commit #d6a422c * update version nr for bioconda * Update README.md * Update README.md --------- Co-authored-by: Ines Scheller <[email protected]> Co-authored-by: Nick <[email protected]> Co-authored-by: Christian Mertes <[email protected]> Co-authored-by: AtaJadidAhari <[email protected]>
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