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Report descriptions - #8

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Report descriptions#8
AntonieV wants to merge 40 commits into
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report_descriptions

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@AntonieV

@AntonieV AntonieV commented Jun 16, 2021

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Description for plots used in report added, changes on deseq2 for comparisons of samples across the groups from each antibody, adaptations for snakemake workflow catalog, cleanup configs, README and ToDo's

@dlaehnemann dlaehnemann left a comment

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Great work, thanks a bunch!

I did not manage to go through everything, yet, but wanted to at least release this batch of comments. I should be approximately half way through...

Comment thread .test/config/config.yaml Outdated
Comment thread .test/config/config.yaml
Comment thread .test/config/units.tsv Outdated
Comment thread .test/config_paired_end/config.yaml Outdated
Comment thread config/README.md Outdated
Comment thread workflow/report/plot_deseq2_FDR_1_perc_MA.rst Outdated
Comment thread workflow/report/plot_deseq2_FDR_1_perc_MA.rst Outdated
Comment thread workflow/report/plot_heatmap_deeptools.rst Outdated
Comment thread workflow/report/plot_macs2_qc.rst Outdated
Comment thread workflow/report/plot_profile_deeptools.rst Outdated
Comment thread workflow/report/plot_quality_by_cycle_picard_mm.rst Outdated
Comment thread workflow/rules/consensus_peak_analysis.smk Outdated
Comment thread workflow/rules/consensus_peak_analysis.smk
Comment thread workflow/rules/consensus_peak_analysis.smk Outdated
Comment thread workflow/report/plot_heatmap_deeptools.rst Outdated

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Once again, great work. And some more suggestions on the second half of this pull request. This is looking really good. We just have to clean up a bit more and we'll finally have that exemplary reimplementation of a nextflow workflow! 🎉

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Comment thread workflow/scripts/featurecounts_deseq2.R Outdated
Comment thread workflow/scripts/featurecounts_deseq2.R Outdated
Comment thread workflow/scripts/featurecounts_deseq2.R
@AntonieV

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Thank you very much for the review and the many great suggestions!

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Thanks again for this major effort. And here finally comes my review. This all looks very good, and any remaining suggestions are either just formatting to improve readability or wording changes to make the report even clearer. Just two actual questions, I think. So we're almost done!

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Comment thread .test/config_paired_end_reduced/config.yaml Outdated
Comment thread workflow/scripts/featurecounts_deseq2.R Outdated
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Comment thread workflow/scripts/featurecounts_deseq2.R Outdated
AntonieV and others added 15 commits February 2, 2022 00:00
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
AntonieV and others added 13 commits February 2, 2022 19:09
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
@AntonieV

AntonieV commented Feb 3, 2022

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Thank you very much for reviewing the PR and the great and helpful suggestions!

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