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Merge main into wilms azimuth branch #851

Merged
merged 165 commits into from
Nov 4, 2024
Merged

Merge main into wilms azimuth branch #851

merged 165 commits into from
Nov 4, 2024

Commits on Oct 7, 2024

  1. Included initial exploratory analysis notebook

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Commits on Oct 8, 2024

  1. storing the module score in seu object

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  2. add script for copykat exploration

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Commits on Oct 9, 2024

  1. copykat exploration plot

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Commits on Oct 10, 2024

  1. update exploration for copykat results

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  2. cluster evaluation

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Commits on Oct 11, 2024

  1. added count on top of each bar

    @UTSouthwesternDSSR
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  2. update renv.lock

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Commits on Oct 15, 2024

  1. added merging part for samples without B cell

    @UTSouthwesternDSSR
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  2. update results readme

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  3. Merge branch 'AlexsLemonade:main' into main

    @UTSouthwesternDSSR
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  4. Apply suggestions from code review 

    Co-authored-by: Joshua Shapiro <[email protected]>
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  5. add copycat scripts

    @JingxuanChen7
    JingxuanChen7 committed Oct 15, 2024
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  6. add infercnv notebook

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Commits on Oct 16, 2024

  1. update docs

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  2. Merge branch 'AlexsLemonade:main' into JingxuanChen7/wilms14_cnv

    @JingxuanChen7
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  3. Start exploring infercnv results

    @maud-p
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  4. update notebook README.md file

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  5. Update README.md

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Commits on Oct 17, 2024

  1. re arrange explore folder

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  2. Merge remote-tracking branch 'origin/JingxuanChen7/wilms14_cnv' into … 

    …JingxuanChen7/wilms14_cnv
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  3. Merge branch 'main' into JingxuanChen7/wilms14_cnv

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  4. update scripts

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  5. Merge remote-tracking branch 'origin/main' into UTSouthwesternDSSR/no… 

    …nETP
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  6. update structure and filename

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  7. add B cell ScType score for Bcells from different methods

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  8. apply review suggestions

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Commits on Oct 18, 2024

  1. added new B cells part

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  2. changes to PR#828

    @maud-p
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  3. add install instructions and a future usage section

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  4. say forthcoming

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  5. Merge branch 'main' into sjspielman/821-ropenscpca-install-instructions

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  6. Merge branch 'main' into JingxuanChen7/wilms14_cnv

    @sjspielman
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  7. Update packages/rOpenScPCA/README.md 

    Co-authored-by: Joshua Shapiro <[email protected]>
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  8. Merge pull request AlexsLemonade#833 from sjspielman/sjspielman/821-r… 

    …openscpca-install-instructions

Add rOpenScPCA install instructions
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  9. update parameters for stability function

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  10. update renv.lock

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  11. Merge branch 'main' into JingxuanChen7/wilms14_cnv

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  12. writing newB cells for running inferCNV

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  13. Merge pull request AlexsLemonade#825 from JingxuanChen7/JingxuanChen7… 

    …/wilms14_cnv

Exploratory CNV notebook for Wilms tumor annotation (SCPCP000014)
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  14. Merge branch 'main' into main

    @jaclyn-taroni
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  15. Merge pull request AlexsLemonade#815 from UTSouthwesternDSSR/main 

    Attempt to identify tumor cells in those non-ETP samples without B cells (SCPCP000003)
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  16. add SCT as an option

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  17. edit prediction path due to folder structure change

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  18. check png plots

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  19. Merge branch 'AlexsLemonade:main' into JingxuanChen7/wilms14_anchor2

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Commits on Oct 19, 2024

  1. PR#828 Add corrected html notebooks

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  2. corrections PR#828

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Commits on Oct 21, 2024

  1. Add files via upload

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  2. re arrange old plots & update doc

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  3. Merge remote-tracking branch 'origin/JingxuanChen7/wilms14_anchor2' i… 

    …nto JingxuanChen7/wilms14_anchor2
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  4. update doc

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  5. add glmGamPoi for SCTransform

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  6. improve PR#828 and try inter-patient normal reference

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Commits on Oct 22, 2024

  1. Adding the renv and ancillary files

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  2. updated the notebooks 

    updated the notebook to include plot outputs
updated the reference to include papers and internal reference
    @danhtruong
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  3. Update analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  4. Update analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  5. Update analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  6. Update analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  7. Update analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  8. Update analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  9. Update analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  10. updated the notebooks 

    updated the notebook to include plot outputs
updated the reference to include papers and internal reference
added plot outputs
    @danhtruong
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  11. updated the notebooks 

    updated the notebook to include plot outputs
updated the reference to include papers and internal reference
added plot outputs
    @danhtruong
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  12. update threshold exploration

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  13. update threshold exploration

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Commits on Oct 23, 2024

  1. Apply suggestions from code review 

    modified the saves

Co-authored-by: Joshua Shapiro <[email protected]>
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  2. Apply suggestions from code review 

    modified the saves

Co-authored-by: Joshua Shapiro <[email protected]>
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  3. Apply suggestions from code review 

    modified the saves

Co-authored-by: Joshua Shapiro <[email protected]>
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Commits on Oct 24, 2024

  1. Revert "Apply suggestions from code review " 

    This reverts commit 58eda51, reversing
changes made to b16d3d4.
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  2. Merge remote-tracking branch 'upstream/main' into danhtruong/cell-typ… 

    …e-dsrct
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  3. Merge pull request AlexsLemonade#794 from danhtruong/danhtruong/cell-… 

    …type-dsrct

Included initial exploratory analysis notebook
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Commits on Oct 25, 2024

  1. Add separate zellkonverter intialization

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  2. Don't use SCT in testing

    @jashapiro
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  3. add glmGamPoi for SCTransform

    @JingxuanChen7 @jashapiro
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  4. Add the dockerfile

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Commits on Oct 28, 2024

  1. Merge pull request AlexsLemonade#841 from jashapiro/docker_for_wilms 

    Add docker image for cell-type-wilms-tumor-14
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  2. Merge branch 'main' into JingxuanChen7/wilms14_anchor2

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  3. apply suggestions

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  4. Update README.md file

    @maud-p
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  5. update notebook and reports

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  6. Update README.md file

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  7. add ggdist dependencie

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  8. Merge pull request AlexsLemonade#9 from maud-p/origin/06_explore_infe… 

    …rcnv

add ggdist dependencie
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  9. Update README.md

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  10. Delete analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration.html
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  11. Delete analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration_mappingscore_threshold_0.5.html
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  12. Delete analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration_mappingscore_threshold_0.75.html
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  13. Delete analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration_mappingscore_threshold_0.85.html
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  14. Delete analyses/cell-type-wilms-tumor-06/notebook/04_annotation_Acros… 

    …s_Samples_exploration_mappingscore_threshold_0.95.html
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  15. update mapping_score --> predicted.score

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  16. update mapping --> predicted.score

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  17. update param argument mapping --> predicted.score

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  18. update params for "04_annotation_Across_Samples_exploration.Rmd" mapp… 

    …ing --> predicted
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  19. few changes to PR828

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  20. few changes to PR828

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  21. Merge pull request AlexsLemonade#10 from maud-p/origin/06_explore_inf… 

    …ercnv

Origin/06 explore infercnv
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  22. update notebook

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  23. Merge pull request AlexsLemonade#11 from maud-p/origin/06_explore_inf… 

    …ercnv

update notebook
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Commits on Oct 29, 2024

  1. add comment on 06_infercnv.R on saved output

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  2. Merge pull request AlexsLemonade#12 from maud-p/origin/06_explore_inf… 

    …ercnv

add comment on 06_infercnv.R on saved output
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  3. apply suggestions & create sum table

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  4. Update the main README.md file

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  5. update doc

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  6. Merge branch 'main' into 04_explore_mapping_score

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  7. Merge branch 'main' into 06_explore_infercnv

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  8. Update analyses/cell-type-wilms-tumor-06/scripts/06_infercnv.R 

    Co-authored-by: Stephanie Spielman <[email protected]>
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  9. Update analyses/cell-type-wilms-tumor-06/scripts/06_infercnv.R 

    Co-authored-by: Stephanie Spielman <[email protected]>
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  10. Update analyses/cell-type-wilms-tumor-06/scripts/06_infercnv.R 

    Co-authored-by: Stephanie Spielman <[email protected]>
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  11. Update analyses/cell-type-wilms-tumor-06/scripts/06b_build-normal_ref… 

    …erence.R

Co-authored-by: Stephanie Spielman <[email protected]>
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  12. Update analyses/cell-type-wilms-tumor-06/scripts/06_infercnv.R 

    Co-authored-by: Stephanie Spielman <[email protected]>
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  13. Update analyses/cell-type-wilms-tumor-06/scripts/06b_build-normal_ref… 

    …erence.R

Co-authored-by: Stephanie Spielman <[email protected]>
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  14. Update analyses/cell-type-wilms-tumor-06/notebook_template/06_cnv_inf… 

    …ercnv_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  15. apply review comments

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  16. Merge pull request AlexsLemonade#835 from maud-p/04_explore_mapping_s… 

    …core

04- Explore the mapping scores for Wilms tumor -06
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  17. update docs

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  18. Merge branch 'main' into JingxuanChen7/wilms14_anchor2

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  19. update html reports

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  20. Merge pull request AlexsLemonade#13 from maud-p/06_updated_branch2 

    update html reports
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  21. Merge branch 'main' into 06_explore_infercnv

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  22. Merge pull request AlexsLemonade#828 from maud-p/06_explore_infercnv 

    06 explore infercnv for Wilms tumor -06
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  23. Merge branch 'main' into JingxuanChen7/wilms14_anchor2

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  24. Draft annotation

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Commits on Oct 30, 2024

  1. added words to dictionary

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  2. Merge pull request AlexsLemonade#836 from JingxuanChen7/JingxuanChen7… 

    …/wilms14_anchor2

Adding SCTransform as an alternative to anchor transfer-Wilms tumor annotation (SCPCP000014)
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  3. Merge branch 'main' into sjspielman/809-some-spelling

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  4. Update analyses/cell-type-wilms-tumor-06/notebook/07_annotation_Acros… 

    …s_Samples_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  5. Update analyses/cell-type-wilms-tumor-06/notebook/07_annotation_Acros… 

    …s_Samples_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  6. Update analyses/cell-type-wilms-tumor-06/notebook/07_annotation_Acros… 

    …s_Samples_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  7. Update analyses/cell-type-wilms-tumor-06/notebook/07_annotation_Acros… 

    …s_Samples_exploration.Rmd

Co-authored-by: Stephanie Spielman <[email protected]>
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  8. changes to PR844

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Commits on Oct 31, 2024

  1. add rough tumor classification

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  2. add default column & fix ci

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  3. Add infercnv and 07 notebook steps to the workflow script

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  4. merge main

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  5. remove workflow script that ended up in top level directory

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  6. Remove old notebook

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  7. the notebook uses both, not pull

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  8. Merge pull request AlexsLemonade#845 from sjspielman/sjspielman/809-s… 

    …ome-spelling

Add words to dictionary
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  9. apply comment

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  10. ensure unique only to prevent duplicate runs

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  11. Merge branch 'main' into edit_result_table

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  12. fix bug in infercnv script that prevented samples from running with '… 

    …both' if they dont have both immune and epithelial
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  13. add additional check needed for infercnv that there is at least 1 nor… 

    …mal cell if a reference is being used. also, added seed which was missing
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  14. Merge pull request AlexsLemonade#846 from JingxuanChen7/edit_result_t… 

    …able

Add rough tumor classification into the result table-Wilms tumor annotation (SCPCP000014)
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  15. fix order of logic

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  16. update code to create a final table of annotations

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Commits on Nov 1, 2024

  1. add recommended option

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  2. some README updates

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  3. fix colon bug in 06 notebook

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  4. only loop over relevant sample ids, and clean up the 07 notebook steps

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  5. render final notebook

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  6. update notebook readme

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  7. Merge branch 'main' into 06_updated_branch2

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  8. Include infercnv results for SCPCS000190 by using none as a reference… 

    …, so we can get some draft annotations for it
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  9. Update base image

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  10. add seed even though not used, so include note to that effect

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  11. need dashes

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  12. Merge pull request AlexsLemonade#850 from jashapiro/jashapiro/hello-p… 

    …ython-docker

Update hello-python docker image
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  13. Found infercnv argument to get infercnv running for the sample with t… 

    …he missing annotations, and updated code accordingly to run this sample
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  14. only map over relevant sample ids, and knit updated notebook

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  15. Merge branch 'main' into 06_updated_branch2

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  16. Merge pull request AlexsLemonade#844 from maud-p/06_updated_branch2 

    Draft annotation
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  17. Merge main and fix conflicts

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