Add spatiotemporal SETBP1 target permutation analysis - #9

Merged

lizzyjoan merged 195 commits into

mainfrom

Apr 10, 2026

Commits on Mar 4, 2025

Update README.md with data sets
lizzyjoan
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68a35da
reorder scripts
lizzyjoan
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c728c27
rm scripts not necessary for downloads
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d911982
megalinter adjustments
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ae9ae8e

Commits on Mar 5, 2025

rm unnecessary script for data download
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f7e8347

Commits on Mar 21, 2025

split download by dataset
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08f354c
rm aggregated SRR list and test list
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d528dd3

Commits on Mar 26, 2025

updated human gencode annotation
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7d68ef6

Commits on Mar 28, 2025

create conda env from yml if needed
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69361ac
fix lint spellcheck error by adding double quotes to prevent globbing and word splitting
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d6e0c5d
fix mouse reference
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b4d9c0a

Commits on Apr 4, 2025

removed SRA IDs for non-RNAseq files from Shaw dataset
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c111db1

Commits on Apr 8, 2025

simplified path using CAP_CONDA_PATH
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d79beb9
update symlink paths
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74da99e
separate conda env setup from data download
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d50c353

Commits on Jun 11, 2025

fixed new 'disk limit exceeded' error
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83801af
rm unnecessary code leftover from splitting conda and fetch data scripts
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c88e04f

Commits on Jun 12, 2025

switch from conda to docker for sra-toolkit
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14e19b3

Commits on Jun 13, 2025

parallelize gzipping across threads to reduce time
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989647f
fix linting error
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b4a8748
add script to run md5 checksums on fastq files
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7f4c329
fixing lintr error
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5d99ea6

Commits on Jul 24, 2025

prefetch before fastq dump
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d97bfaf

Commits on Jul 25, 2025

rm timestamp from gzipping, causing MD5's not to match
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3b5cd37
updated verifications after fixing gzip timestamping
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d4655e1
typo in print message
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951dad0

Commits on Jul 30, 2025

rm unused scripts
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9718256
set array back to 0-2 and fix indention
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e121b65

Commits on Sep 5, 2025

Merge pull request #1 from lasseignelab/datadownload
lizzyjoan
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c38f50a

Commits on Sep 23, 2025

Merge branch 'main' into preprocess
lizzyjoan
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1a329b3
Merge pull request #2 from lasseignelab/preprocess
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b4cb016
merge updates from main to eda
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a970a14
rm dead code
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f731182
rm broken logo link
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e6f1f2c
fix typo for str_wrap in rse_pca
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ed251ff
update to run with job script
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6ab2f42
fix linting
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1ffb5aa

Commits on Oct 22, 2025

resolved 0 dimension svd error
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1b7af01
rm old files
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0cd55b3
cleanup code, rm Bioproject as feature to color by (redundant with 'author' feature)
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cab3666
fixed ordering for plot names
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aab5fe2
update docker image to use to minimize number of images to pull and convert
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db7a0bb
fresh run with updated container, rm old files
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d731676
fresh run with updated container, rm old files
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1af24c0
verifications for EDA output file MD5's
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f65b729

Commits on Oct 27, 2025

lint and styled
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1f729ef
fix lint errors, rm unused functions
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9971a80
fix linter errors
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5b356c2
fix linter errors
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09d6a6a
issue between specific version of megalinter and purrr
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012b040

Commits on Oct 28, 2025

Commits on Nov 11, 2025

Update 05_data_cleaning.R
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e54af8e
Update 06_dataset_eda.R
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1aa3537
Update 06_dataset_eda.R
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4f64a70
Update 07_combined_eda.R
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8d38bf9

Commits on Nov 17, 2025

fixed print statement
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e6f6044
fixed error introduced by updated variable name in for loop
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e026a8b
updated md5 checksums for verifying reproducibility
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37d3876
Merge branch 'main' into dea
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8b2445d
split differential expression analysis into 2 scripts
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de78310
fix order of code--composite scoring before comparison of methods
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6f8d0b0
updated script name
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08d1714
increase sensitivitiy for significance by lowering p-adj val threshold to 0.1 (prev 0.05)
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2c0a787

Commits on Nov 18, 2025

code cleanup, fresh run
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f03a382
simplify code, add trycatch for contrasts with no ORA results, and fix filepaths
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a8842cd
lint and style
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e151e68
update script names
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3812a83

Commits on Nov 19, 2025

fixed typo to print ora_down plots
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8853cce
cleanup consensus signature method comparisons
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b0b6867

Commits on Nov 20, 2025

compare enriched terms resulting from ORA of > 1 signature
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5654963

Commits on Nov 21, 2025

Commits on Nov 24, 2025

add entrez gene mapping, prioritize signatures by entrez-mappable genes for downstream analysis
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283c755

Commits on Nov 25, 2025

fixed entrez gene mapping to avoid duplications, expanded signature size to top 300
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ec3a8f5

Commits on Dec 1, 2025

fixed print message
lizzyjoan
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cab29f8
lint and style
lizzyjoan
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b62a95b
add job script, cleanup print statements, rm setbp1 targets comparison
lizzyjoan
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848eed9
improve commenting and filenames, rm dead code
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cb38aa2
fix lab logo image link
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844ed5a
simplify matrix-prep with function
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80831ce
updated filenames
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1d903bc
add verifications for code review
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f234389
add seed
lizzyjoan
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6abcbdc
Update mega-linter.yml
lizzyjoan
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e110835
Update mega-linter.yml
lizzyjoan
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9e51389
fix lintr errors
lizzyjoan
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f6f0dd7
explicit function imports and declaring global variables to avoid lintr errors
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372ae16
explicit importing and setting variables still gave lintr errors -- skip object_usage_linter
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4f8d6bb
Update README.md
lizzyjoan
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700fdd5
trying to disable object_usage_linter
lizzyjoan
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1d78e8a
troubleshooting lintr
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4afba72
troubleshooting lintr
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60f1439
fix indention spacing
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afe07a7

Commits on Dec 2, 2025

save ORA outputs, tweak combined terms plot for legibility
lizzyjoan
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7447f9c

Commits on Dec 10, 2025

Commits on Dec 16, 2025

Merge pull request #4 from lasseignelab/eda
lizzyjoan
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ad416bc

Commits on Dec 17, 2025

adding creating dataframe file
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cc4daf0
adding creating dataframe file
sashataluri
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41d20eb

Commits on Feb 23, 2026

Add files via upload
sashataluri
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f9deee8
Add files via upload
sashataluri
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1bc0f97

Commits on Mar 4, 2026

fix inconsistent variable names
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b505359
fix inconsistent variable names
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e0ebc14
fix inconsistent variable names
lizzyjoan
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655328e
exploring brainspan metadata for donor counts by age
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e837ea3
exploring brainspan metadata for donor counts by age
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cb85008
ignore large (>100mb) file
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2fcc671
run permutations by developmental windows (vs just prenatal/postnatal)
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0e91d67
add target brain regions to permutation analysis
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05bfcb0
add permutations by relevant brain regions
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cf242c7
adjusted age windows to increase sample size, with emphasis on rapid synaptogenesis (birth-1 year) and synaptic pruning (2-16 years old)
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26a5cba
fix filter for infancy age window
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f192596
normalize and scale brainspan's RPKM counts
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2cd4713
rm zero variance genes prior to scaling
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19cb833
switched back to all brain regions to help increase n
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ec8985a
return observation values for target genes in each window
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8acd89f
fix format of returned gene means by window
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c93710b
fresh run for target prioritization
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3427d8b
fix rownames and colnames for gene means table
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829b5ce

Commits on Mar 5, 2026

Commits on Mar 6, 2026

force push setbp1 targets involved in select pan-go pathways
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53a2936
rm dead code
lizzyjoan
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11b84dd

Commits on Mar 9, 2026

Commits on Mar 10, 2026

resolved errors for reading in large count data, updated metadata for consistency, and troubleshooting saving plots with SETBP1 target expression means
lizzyjoan
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e236188

Commits on Mar 11, 2026

update wrangling for log transformation and target means
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6817d3d

Commits on Mar 12, 2026

Commits on Mar 13, 2026

trying to resolve issue with adult GTEx -- only reading in 594 genes
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db6f8af

Commits on Mar 16, 2026

Commits on Mar 17, 2026

barplot to lollipop plot, increase axis limits, flip x y coordinates
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cb25eac
split brainspan permutations and plotting into separate scripts
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3c500a6
tweak plot for asthestics
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aabb38a
combine dGTEx ages together to increase statistical power -- very few/missing representation of some tissues at specific time points
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33496ba
split permutation analysis and plotting into separate scripts
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2ee0c5f
set consistent colors for plot up/down values
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fd21208
combine plots for supplementary figure 1
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39658e5
combine, cleanup, and move plots and plotting scripts
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86ae51a
increase to 10000 permutations
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c8f434b
add target exp wilcox comparison by sex
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93cafd0
fix age bins for plotting expression by sex
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3e948b2

Commits on Mar 27, 2026

Commits on Mar 31, 2026

rm unnecessary scripts for this PR
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e29951b
fix linter errors
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f18580c
update dGTEx files (were switched from txt to xlsx on GTEx)
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0be9885
update subfolders for adult/dev gtex, update print statements
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de7cb3a
verify data downloads
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83c8650
update directories and cleanup print statements
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9a0cbce
update filenames and print statements
lizzyjoan
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caf1382
add brainspan/gtex symlinks
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1cf103d
update gtex symlink
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dafd1fc

Commits on Apr 1, 2026

Commits on Apr 3, 2026

update run with updated SETBP1 targets
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f459f96
update verification
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f4055e8

Commits on Apr 6, 2026

update setbp1 targets file
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4992523
rm redundant line for checking/making directory
lizzyjoan
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de2857d

Commits on Apr 7, 2026

Commits on Apr 8, 2026

increase slurm time request to deal with user-user variability on Cheaha HPC
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d8b8f01