Signature reversion and drug analyses - #8

Merged

lizzyjoan merged 184 commits into

mainfrom

May 1, 2026

Commits on Nov 24, 2025

initial exploration with signaturesearch
lizzyjoan
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df2f956
initial exploration with signaturesearch
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5a0ece6
Update signatures by prioritizing ENTREZ-mappable genes (required for signatureSearch to query LINCS)
lizzyjoan
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b85bfe0
Update signatures by prioritizing ENTREZ-mappable genes (required for signatureSearch to query LINCS)
lizzyjoan
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18f480b
annotate LINCS drugs, analyze signature reversion results
lizzyjoan
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e780823
annotate LINCS drugs, analyze signature reversion results
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c9a37e8

Commits on Nov 25, 2025

drug target analyses
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389dc59
drug target analyses
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0afe1bb
cleanup code, comment out argparse for nvim interactive coding
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4df6dd2
cleanup code, comment out argparse for nvim interactive coding
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501f07c
prep for analyzing other signatures from otehr methods
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c94a02c
prep for analyzing other signatures from otehr methods
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4f6f76e
rm accidental file
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rm accidental file
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3e14ca9
Merge branch 'dea' of github.com:lasseignelab/setbp1_hd into sigsearch
lizzyjoan
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a8f769b
Merge branch 'dea' of github.com:lasseignelab/setbp1_hd into sigsearch
lizzyjoan
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6575b4b
updated run with fixed signatures
lizzyjoan
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7f4dd47
updated run with fixed signatures
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120ea0f
run signaturesearch with meta analysis signature (instead of composite score signature)
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ce68020
run signaturesearch with meta analysis signature (instead of composite score signature)
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ae2f1d7
analysis for each method signature and fixed filenames
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3d69c35
analysis for each method signature and fixed filenames
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d590240

Commits on Dec 1, 2025

Commits on Dec 2, 2025

Commits on Dec 3, 2025

further exploration of drug targets:
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a165b18
further exploration of drug targets:
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83a22eb
rm dea verifications -- seperate PR
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31d5efb

Commits on Dec 4, 2025

Commits on Dec 8, 2025

comparing to 'core genes' indicated in previous studies and added covariate by dataset for meta analysis
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df9995c

Commits on Dec 10, 2025

add wong et al DEGs for validation
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597ab3b
save meta analysis logFC with RRA for directionality, updated arg parse
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9b1c5e4
Merge branch 'consensus' of github.com:lasseignelab/setbp1_hd into sigsearch
lizzyjoan
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4d01a2e
Merge branch 'consensus' of github.com:lasseignelab/setbp1_hd into sigsearch
lizzyjoan
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6518a38
run with updated RRA signature
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1b03795
run with updated RRA signature
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6faebea
simplify ORA code, improve plots
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7d7e48d

Commits on Dec 11, 2025

Commits on Dec 12, 2025

Commits on Dec 14, 2025

returned to RRA without splitting by direction first
lizzyjoan
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779d1ab
simplify code, rm dead code
lizzyjoan
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4aadfe6

Commits on Dec 15, 2025

rearrange code, improve variable names
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e79fa11
update filenames, clean up old files
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e75b3d3
update filenames, clean up old files
lizzyjoan
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b0415a4
cleanup plots, files
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a6bc336
Merge branch 'main' of github.com:lasseignelab/setbp1_hd into consensus
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a36fc28
fresh run after merging main
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a6668d4
rm msigdb download -- switched to pulling genesets via gprofiler2
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fa6a8e5
add number for selecting top n DEGs by method as a user argument
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6d1bd41
update for symlinking wong data
lizzyjoan
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dcb7881
Merge branch 'consensus' of github.com:lasseignelab/setbp1_hd into sigsearch
lizzyjoan
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ebcb038
Merge branch 'consensus' of github.com:lasseignelab/setbp1_hd into sigsearch
lizzyjoan
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4f1602e
running with RRA signature without direction-splitting prior to RRA
lizzyjoan
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00c6f10
running with RRA signature without direction-splitting prior to RRA
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6306dd8

Commits on Dec 17, 2025

moved files around, added slurm job script, removed dead code
lizzyjoan
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f04da86
moved files around, added slurm job script, removed dead code
lizzyjoan
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852fd78
rm old remnant code
lizzyjoan
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b07adf7
Merge branch 'main' of github.com:lasseignelab/setbp1_hd into consensus
lizzyjoan
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83992d3
clean up filenames and plots
lizzyjoan
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bb67ca9
clean up filenames and plots
lizzyjoan
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e2e55f6

Commits on Jan 6, 2026

Commits on Jan 8, 2026

update run with updated consensus signature
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815db67
update run with updated consensus signature
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e82b22f
analyze drug target results
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a83d5ee
analyze drug target results
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0322579

Commits on Jan 16, 2026

attempt to pull dailymed data for a set of test drugs
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b1e68d2
attempt to pull dailymed data for a set of test drugs
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eac325c

Commits on Jan 20, 2026

more specific searching for sections and keywords
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60e5443
more specific searching for sections and keywords
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3f3203c

Commits on Jan 26, 2026

Commits on Feb 3, 2026

update gitignore

Lizzy Wilk
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Lizzy Wilk
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a5f9e71
update gitignore

Lizzy Wilk
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Lizzy Wilk
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7a54de0
linting, formatting

Lizzy Wilk
authored and
Lizzy Wilk
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dc98760
linting, formatting

Lizzy Wilk
authored and
Lizzy Wilk
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0a89573
linting, formatting

Lizzy Wilk
authored and
Lizzy Wilk
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c0158ca
linting, formatting

Lizzy Wilk
authored and
Lizzy Wilk
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e52cf66

Commits on Feb 4, 2026

lint and style
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6717b01
lint and style
lizzyjoan
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11eaf85
linting and formatting

Lizzy Wilk
authored and
Lizzy Wilk
committed
0b19d56
linting and formatting

Lizzy Wilk
authored and
Lizzy Wilk
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efc2b77
linting and formatting

Lizzy Wilk
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Lizzy Wilk
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042693e
linting and formatting

Lizzy Wilk
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Lizzy Wilk
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892a2d0
linting and formatting

Lizzy Wilk
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Lizzy Wilk
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ba5e2fa
linting and formatting

Lizzy Wilk
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Lizzy Wilk
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65a6549
linting and formatting

Lizzy Wilk
authored and
Lizzy Wilk
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25528d2
linting and formatting

Lizzy Wilk
authored and
Lizzy Wilk
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89095c9
lint and style
lizzyjoan
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9c7e2d7
lint and style
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7fc171e
lint and sytle
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ead0273
lint and sytle
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82aacf5

Commits on Feb 9, 2026

Commits on Feb 11, 2026

add verification for sigsearch results
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0c2631e
add verification for sigsearch results
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c659a52
format and lint
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270ce6d
format and lint
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9a5a8ae

Commits on Feb 12, 2026

move plotting script
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c46695b
move plotting script
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9ed148e
compile figure 5
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fbcf719
compile figure 5
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4677b6c
fix lintr errors
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2903d97
fix lintr errors
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5820134
update comments and filepaths
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e5c1ae4
update comments and filepaths
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af2c6a5
update file and variable neames
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f860818
update file and variable neames
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3221e7b
combine DailyMed safety data with drug annotations
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a15bc46
combine DailyMed safety data with drug annotations
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db322ad
update filenames, add slurm script
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7b6a932
update filenames, add slurm script
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bd6688e
cleanup commenting and print messages
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f16d497
cleanup commenting and print messages
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01c39ba
rm old files
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a202fe3
rm old files
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1709b77

Commits on Feb 13, 2026

rm old files
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a88b7f2
rm old files
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e84d9bf
updated files
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4711b09
updated files
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6301d4f
make log messages prettier
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a96f76c
make log messages prettier
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112dc83
rm old files
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5efcd3e
rm old files
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efa4fc1
ignore helper lint/style script
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1696ef1
ignore helper lint/style script
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a1b67e1
ignore helper lint/style script
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67e91a1
ignore helper lint/style script
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fd40b8c
swapped plot, updated filenames
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3dbba03
swapped plot, updated filenames
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77321e0

Commits on Feb 17, 2026

force push SETBP1 target lists
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168a1aa
force push SETBP1 target lists
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c626e27
rm unused and redundant code
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7cf761c
rm unused and redundant code
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6fc8a7a

Commits on Feb 19, 2026

rm unnecessary code
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fa9de22
rm unnecessary code
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be6da26
add non-reproducible disclaimer for DailyMed API use
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828efb7
add non-reproducible disclaimer for DailyMed API use
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9cbe0f8
API outputs not reproducible--removed verification
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9e7a72a
API outputs not reproducible--removed verification
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b2e07f4

Commits on Mar 9, 2026

Commits on Apr 1, 2026

ignore lintr/styler helper script
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9145e90

Commits on Apr 2, 2026

run with updated SETBP1 targets + prioritized targets
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304eb28
add pediatric drug safety excerpts
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fe2b421
run with updated SETBP1 targets + prioritized targets
lizzyjoan
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9b39e6c
update verifications
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9aae5b3
lint and style
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35b18f2
update drug safety filepath
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6b4ccbd
update safety data run and filepath
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e15d9aa
update safety data run and filepath
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0956053
fix filepath to rm redundancy
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389a583
fix linter error
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5368f69

Commits on Apr 3, 2026

update full SETBP1 targets list
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6635091

Commits on Apr 10, 2026

Commits on Apr 14, 2026