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Report descriptions #8

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AntonieV
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@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 reviewed Jun 25, 2021
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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...

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dlaehnemann
dlaehnemann reviewed Jun 28, 2021
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dlaehnemann requested changes Jun 28, 2021
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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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Thank you very much for the review and the many great suggestions!

dlaehnemann
dlaehnemann reviewed Jan 21, 2022
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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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AntonieV and others added 15 commits February 2, 2022 00:00
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Update .test/config/config.yaml
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Update .test/config/config.yaml
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Update .test/config_paired_end/config.yaml
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Update .test/config_paired_end/config.yaml
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Update .test/config_paired_end_reduced/config.yaml
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Update .test/config_single_end/config.yaml
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Update .test/config_single_end/config.yaml
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Update .test/config_single_end_reduced/config.yaml
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Update .test/config_single_end_reduced/config.yaml
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Update workflow/report/plot_consensus_peak_intersect.rst
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Update config/config.yaml
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Update config.yaml
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Update workflow/report/plot_deseq2_FDR_1_perc_MA.rst
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Update workflow/report/plot_deseq2_FDR_1_perc_volcano.rst
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Update workflow/report/plot_deseq2_FDR_5_perc_MA.rst
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AntonieV and others added 13 commits February 2, 2022 19:09
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Update workflow/report/plot_deseq2_FDR_5_perc_volcano.rst
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Update workflow/report/plot_deseq2_heatmap.rst
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Update workflow/scripts/featurecounts_deseq2.R
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Update workflow/scripts/featurecounts_deseq2.R
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Update workflow/scripts/featurecounts_deseq2.R
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Update workflow/scripts/featurecounts_deseq2.R
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Update workflow/scripts/featurecounts_deseq2.R
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Update workflow/report/plot_deseq2_pca.rst
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Update workflow/report/plot_deseq2_sample_corr_heatmap.rst
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Update workflow/report/plot_deseq2_scatter.rst
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Update workflow/report/plot_heatmap_deeptools.rst
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Update workflow/report/plot_macs2_qc.rst
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Update workflow/report/plot_profile_deeptools.rst
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AntonieV commented Feb 3, 2022

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

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