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Include dsb step #13

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Include dsb step #13

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aricht
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@aricht aricht commented Dec 5, 2023

Description

Please include a summary of the change.

Type of change

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • A documentation update

Has the appropriate test been performed?

  • Feature test has been performed
  • A pipeline test has been performed

Checklist:

  • The code follows common style guidelines (linting your code is highly recommended)
  • The code is commented reasonably
  • The documentation has been updated
  • CHANGELOG.md is updated.
  • README.md is updated

Anne Bertolini added 17 commits October 9, 2023 14:05
[FEAT] Add new script dsb_normalize_adt.R
08810d9 
Add script that performs dsb normalization of ADT counts.
Script covers normalization without isoform controls.
Will be applied to single sample, without hashing.
[WIP] Add copy of analyse_citeseq.R to be adapted to dsb normalization
57908e0
[DOC] Run "style_file" on analyse_citeseq_after_dsb.R
0b5a7bc
[FEAT] Adapt script analyse_citeseq_after_dsb.R
ea037bc 
- remove any functionality about thresholds
- make sure that the dsb normalized ADT counts that can be 0 are set to
  0 to not break the clustering
- save the SCE object including BREMSC clusters, and all UMAP
  coordinates in the colData
- save the colData of the final SCE object as tsv
[FEAT] Include changes with dsb normalization
2a0ef71 
- rename and adapt script analyse_citeseq_dsb.R
- adapt Snakefile_no_hashing to have as default the dsb normalization
[FEAT] Add rule for dsb normalization of ADT counts
4b79958
[FEAT] After cellranger keep compressed and decompressed results
9a8a9c5
[FEAT] Save h5 file in analyse_citeseq_dsb.R
3bfa548 
- save final results as RDS with SCE but also h5 file
[FIX] Include package in script dsb_normalize_adt.R
7169a04 
Forgot `optparse` package in script dsb_normalize_adt.R.
Added.
[FIX] parameter in script analyse_citeseq_dsb.R
1dbaf4f
[WIP] Add draft change CHANGELOG.md
695ada1
[FEAT] Change dsb_normalize_adt to use singularity not conda
6c376c5 
- script `dsb_normalize_adt.R`, from rule `dsb_normalize_adt` uses dsb
package that is not available in conda
- use custom singularity image for this step, instead of conda env
[DOC] Include dsb correction as default step for experiments
9043113 
without hashing deconvolution.
[DOC] Add link to dsb_r-base_4.2.3.sif in README
64a2f63
[DOC] Adapt section about dsb and cellranger in README
a3d7b6d
Merge branch 'main' into include_dsb
8a0c086
[DOC] Beautify rulegraphs
8bdecbe
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@aricht