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Merge main into feature/ropenscpca #769

Merged
merged 61 commits into from
Sep 20, 2024
Merged

Merge main into feature/ropenscpca #769

merged 61 commits into from
Sep 20, 2024

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sjspielman
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Housekeeping, try 2!

maud-p and others added 30 commits September 4, 2024 17:02
@maud-p
Add clustering exploration
48ae7d0
@maud-p
commit renv.lock
a79e243
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
d804a26 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
6e1d08c 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
91ef982 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
b49d44b 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/00_run_workflow.R
d172246 
Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
a26a351 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
9ce209a 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p
Add to PR AlexsLemonade#750
b0e215f
@maud-p
Update README.md
3138336
@jashapiro
Add download option to script
dd84652
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
a211491 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
bfaef24 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
b57eab3 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
b02c340 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
03be050 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
c933ca6 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
7807d95 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
bf533f5 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
d09b863 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
1080e0a 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
80c791c 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p
add to PR AlexsLemonade#750
60d935c
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook/README.md
b1c97fb 
Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook/README.md
1c649f9 
Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
411c3e1 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
d13c9a0 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
394874c 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
1afdddc 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
sjspielman and others added 24 commits September 16, 2024 12:07
@sjspielman
Merge pull request AlexsLemonade#763 from sjspielman/sjspielman/updat…
fbf0d60 
…e-sync-script-download-printing

Update sync-results.py printing
@JingxuanChen7
update doc so far
847bf5a
@JingxuanChen7
Merge branch 'AlexsLemonade:main' into JingxuanChen7/wilms14_pr
30c0c5e
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
9c69a26 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
61753ea 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
f2c289b 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
e9e26c6 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
517d478 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
1294215 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
f0fdc0e 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
a77bbbc 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
eda0dac 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p
Add SCPCS000197 report
fe01572
@JingxuanChen7
rm unnecessary & update readme
487d6e9
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
6c4b012 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@JingxuanChen7
updates on renv, remove conda
8e69621
@maud-p @sjspielman
Update analyses/cell-type-wilms-tumor-06/notebook_template/03_cluster…
67d9c47 
…ing_exploration.Rmd

Co-authored-by: Stephanie Spielman <stephanie.spielman@gmail.com>
@maud-p
update reports
99e11ba
@JingxuanChen7
code review
9be5d74
@JingxuanChen7
resolve comments
1731730
@jashapiro
Merge pull request AlexsLemonade#764 from JingxuanChen7/JingxuanChen7…
75deae2 
…/wilms14_pr

Start an analysis for Wilms tumor annotation (SCPCP000014)
@sjspielman
Merge branch 'main' into 03_Look_into_clustering
8dedcd5
@sjspielman
Merge pull request AlexsLemonade#750 from maud-p/03_Look_into_clustering
a0b76ba 
Wilms tumor 06- clustering exploration
@sjspielman
Merge branch 'main' into sjspielman/main-into-ropenscpca_2024-09-19
2908630
@sjspielman sjspielman mentioned this pull request Sep 19, 2024
Merged
@sjspielman sjspielman removed the request for review from jaclyn-taroni September 19, 2024 20:35
jashapiro
jashapiro approved these changes Sep 19, 2024
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LGTM

@sjspielman sjspielman merged commit 914ce82 into AlexsLemonade:feature/ropenscpca Sep 20, 2024
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@sjspielman @jashapiro @maud-p @JingxuanChen7