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Recent Releases of deepcsa

deepcsa - Complete public release

Include more detailed documentation on deepCSA requirements, steps and outputs, improve code readability among many others.

What's Changed

  • First release by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/289
  • First pre-release merge by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/303
  • Documenting and cleaning by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/299
  • Ensure POSTPROCESSVEPPANEL in output by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/311
  • Update mutation rate to mutation density by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/307
  • fix panel annotation bug by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/313
  • Add more complete docs by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/306
  • Allow gene selection in consensus by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/316
  • general structure updates by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/315

Full Changelog: https://github.com/bbglab/deepCSA/compare/v0.1.0-alpha...v0.2.0-alpha

- Python
Published by FerriolCalvet 7 months ago

deepcsa - First release

First release before re-structuring prefix definitions and lib directory. Version of the pipeline used for the normal bladder urothelium project.

What's Changed

  • VCFs annotated by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/8
  • update by @rblancomi in https://github.com/bbglab/deepCSA/pull/12
  • Add lasts preparations for compute depths subworkflow by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/18
  • Basic mutation preprocessing finished by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/19
  • Basic processing working all subworkflows initialized by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/20
  • Major update deepCSA by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/26
  • add all sections working to date by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/34
  • add depths and panels section by @rblancomi in https://github.com/bbglab/deepCSA/pull/33
  • Add mutation rate subworkflow by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/41
  • 43-remove configuration redundancy by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/44
  • dev/omegamulti by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/51
  • dev/muts2sbs by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/52
  • fix: mutation rate computed with SNVs and indels by @rblancomi in https://github.com/bbglab/deepCSA/pull/61
  • Add mSigHDP by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/63
  • Plot basic summary statistics by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/83
  • fix: handle bedtool offset issue by @FedericaBrando in https://github.com/bbglab/deepCSA/pull/88
  • Add omega global loc by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/90
  • Improve config params focussed by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/91
  • Add mutated epithelium computation (breaking changes) by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/81
  • [FIX] Bedtools merge in CREATECUSTOMBED process by @FedericaBrando in https://github.com/bbglab/deepCSA/pull/92
  • add: panel composition adjusted mutrate and Kb by @rblancomi in https://github.com/bbglab/deepCSA/pull/96
  • Use VAF from all molecules by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/102
  • add: oncodrive3d preprocessing module by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/101
  • Update Oncodrive3D run and add Oncodrive3D plotting module by @St3451 in https://github.com/bbglab/deepCSA/pull/106
  • ADD proportion of mutated genomes from VAF by @koszulordie in https://github.com/bbglab/deepCSA/pull/105
  • 104 add indels method by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/109
  • BREAKING CHANGES Add pileup step in the pipeline by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/111
  • Input BAM for running pileup within the pipeline by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/110
  • add fixes by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/124
  • add positive selection side plots + nextflow version to 24.04 by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/121
  • Add option for custom gene groups in omega by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/127
  • Add option to restrict all analysis to custom BED file by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/130
  • Update the scripts to handle NAs in mutations by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/131
  • Add hotspots to mice by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/134
  • Mice working by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/136
  • Add working for mice, omega for hotspots and omega plotting by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/138
  • Add updates from dev branch before testing by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/140
  • add expected epithelium calculation by @AxelRosendahlHuber in https://github.com/bbglab/deepCSA/pull/141
  • working version in the IRB cluster by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/144
  • Reorganize subworkflows input and fix mutrate bug by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/147
  • Minor fixes in depths by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/154
  • Add fixes for updated omega global loc by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/152
  • Add computation of unbiased VAF by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/158
  • Add cconfigs for CHIP by @andrianovam in https://github.com/bbglab/deepCSA/pull/168
  • fix in BED panel creation from TSV by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/170
  • Add protein2dna mapping by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/211
  • Another fix to omega globalloc by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/209
  • Quick fix to make sample names match by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/219
  • Add dNdScv and expected mutated genomes to dev by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/217
  • Add hotspot annotations by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/218
  • Split notinpanel into two filters by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/222
  • Add cohortnrich_threshold by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/223
  • Add option to compute omega for smaller gene areas (not sites) by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/228
  • CODE-REVIEW | NF lint : Implement topics, fix statement outside top-level declaration by @FedericaBrando in https://github.com/bbglab/deepCSA/pull/232
  • Add comparison per site by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/234
  • CODE-REVIEW | 2nd iteration | NF linting, fix nextflow_schema and configs by @FedericaBrando in https://github.com/bbglab/deepCSA/pull/238
  • fix: update workflow name in configs by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/241
  • Compute omega for TERT by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/239
  • Add site comparison of expected vs observed by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/245
  • Add updated filters to dev by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/249
  • Add optional step to blacklist mutations by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/254
  • Update mutations plot format by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/255
  • Add domain BED automated generation by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/253
  • Add new mutated genomes computation by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/251
  • 260 specific consequence type filters for tert promoter in proportion of mutated epithelium by @koszulordie in https://github.com/bbglab/deepCSA/pull/261
  • Fix incorrect plotting of mutational profile by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/263
  • Define SNP flag based on gnomAD by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/266
  • Create single environment for bin python scripts. by @FedericaBrando in https://github.com/bbglab/deepCSA/pull/267
  • Write all versions of mutational profiles by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/271
  • Separation of artifactual filter from somatic filter by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/280
  • Separate depths script into summary and within gene plotting by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/281
  • Update naming of concatenated matrices by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/283
  • Add HDP signature extraction by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/269
  • Add downsampling and regressions by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/258
  • Add no_filter option working by @FerriolCalvet in https://github.com/bbglab/deepCSA/pull/291

New Contributors

  • @rblancomi made their first contribution in https://github.com/bbglab/deepCSA/pull/12
  • @FedericaBrando made their first contribution in https://github.com/bbglab/deepCSA/pull/88
  • @St3451 made their first contribution in https://github.com/bbglab/deepCSA/pull/106
  • @koszulordie made their first contribution in https://github.com/bbglab/deepCSA/pull/105
  • @AxelRosendahlHuber made their first contribution in https://github.com/bbglab/deepCSA/pull/141
  • @andrianovam made their first contribution in https://github.com/bbglab/deepCSA/pull/168

Full Changelog: https://github.com/bbglab/deepCSA/commits/v0.1.0-alpha

- Python
Published by FerriolCalvet 9 months ago