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Add AUCell notebook for scAdvanced pathway analysis #809

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merged 17 commits into from
Nov 26, 2024
Merged

Add AUCell notebook for scAdvanced pathway analysis #809

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d6e5dfc
Add initial draft of the AUCell notebook
jaclyn-taroni Nov 25, 2024
0ffb4c2
Document plot_recovery_code()
jaclyn-taroni Nov 25, 2024
ce363da
Polish AUCell notebook
jaclyn-taroni Nov 25, 2024
339881e
Merge branch 'jaclyn-taroni/711-use-rms-de' into jaclyn-taroni/806-au…
jaclyn-taroni Nov 25, 2024
d0b8e3d
Add AUCell notebook to render live script
jaclyn-taroni Nov 25, 2024
4497a77
Update renv lockfile
jaclyn-taroni Nov 25, 2024
d33e941
Merge branch 'master' into jaclyn-taroni/806-aucell
jaclyn-taroni Nov 25, 2024
596049f
Spell check fixes; rerun notebook
jaclyn-taroni Nov 25, 2024
dfdf159
Actually save HTML version
jaclyn-taroni Nov 25, 2024
f9efb86
Merge branch 'master' into jaclyn-taroni/806-aucell
jaclyn-taroni Nov 25, 2024
150c17f
Apply suggestions from code review
jaclyn-taroni Nov 26, 2024
501abb2
Respond to review
jaclyn-taroni Nov 26, 2024
917ac6e
Add outsized to dictionary
jaclyn-taroni Nov 26, 2024
9afc87e
Apply suggestions from code review
jaclyn-taroni Nov 26, 2024
0d3ab00
Merge branch 'master' into jaclyn-taroni/806-aucell
jaclyn-taroni Nov 26, 2024
a6aa692
Respond to round 2 of review
jaclyn-taroni Nov 26, 2024
b7e92ac
Apply suggestions from code review
jaclyn-taroni Nov 26, 2024
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7 changes: 7 additions & 0 deletions components/dictionary.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ Adelie
ADT
ADTs
aes
Aibar
al
Alboukadel
alevin
Expand All @@ -25,6 +26,7 @@ astrocyte
astrocytes
astrocytoma
ATAC
AUCell
automagically
Ballereau
BAM
Expand All @@ -33,6 +35,7 @@ barcode
barcodes
Becht
benchmarking
bimodally
bioconductor
bioinformatic
bioinformatics
Expand Down Expand Up @@ -123,6 +126,8 @@ epitopes
ERMS
et
Ewels
EWS
EWSR
exponentiate
ExtractoR
FAC
Expand All @@ -138,6 +143,7 @@ FDR
fgsea
fibrotic
Figshare
FLI
FN
FPKM
frac
Expand Down Expand Up @@ -320,6 +326,7 @@ Optimus
orking
orthotopic
OSCA
outsized
overexpressed
overinterpret
overrepresentation
Expand Down
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