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channels: | ||
- conda-forge | ||
- nodefaults | ||
dependencies: | ||
- polars =0.20.28 | ||
- pyreadr =0.5 | ||
- altair =5.2 | ||
- pyarrow =16.1 | ||
- vegafusion =1.6 | ||
- vegafusion-python-embed =1.6 | ||
- vl-convert-python =1.2 | ||
- jupyter_core =5.7 | ||
- ipykernel =6.29 | ||
- nbconvert =7.14 | ||
- notebook =7.0 | ||
- jupyterlab_code_formatter =1.4 |
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{{ snakemake.params.desc }} | ||
Each point represents a gene, x axis shows the {{ snakemake.params.labels[0] }} effect, y-axis the {{ snakemake.params.labels[1] }} effect (both as log2 fold change). | ||
The color encodes the corresponding q-value. | ||
By clicking on points, their label can be displayed. | ||
Holding the Shift key allows to select or deselect labels for multiple genes. |
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rule meta_compare_diffex: | ||
input: | ||
expand( | ||
"results/sleuth/diffexp/{model}.genes-representative.diffexp.rds", | ||
model=lookup( | ||
dpath="meta_comparisons/{meta_comp}/items/*/model", within=config | ||
), | ||
), | ||
output: | ||
"results/tables/diffexp/meta_compare_{meta_comp}.tsv", | ||
"results/meta_comparison/diffexp/{meta_comp}.json", | ||
log: | ||
notebook="logs/meta_compare_diffexp/{meta_comp}.ipynb", | ||
params: | ||
desc=lookup(dpath="meta_comparisons/{meta_comp}/desc", within=config), | ||
labels=lookup(dpath="meta_comparisons/{meta_comp}/items/*/label", within=config), | ||
conda: | ||
"../envs/pystats.yaml" | ||
notebook: | ||
"../scripts/compare_diffexp.py.ipynb" | ||
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rule meta_compare_enrichment: | ||
input: | ||
expand( | ||
"results/tables/go_terms/{model}.go_term_enrichment.gene_fdr_{gene_fdr}.go_term_sig_study_fdr_{go_term_fdr}.tsv", | ||
model=lookup( | ||
dpath="meta_comparisons/{meta_comp}/items/*/model", within=config | ||
), | ||
gene_fdr=str(config["enrichment"]["goatools"]["fdr_genes"]).replace( | ||
".", "-" | ||
), | ||
go_term_fdr=str(config["enrichment"]["goatools"]["fdr_go_terms"]).replace( | ||
".", "-" | ||
), | ||
), | ||
output: | ||
"results/tables/go_terms/meta_compare_{meta_comp}.tsv", | ||
"results/meta_comparison/go_terms/{meta_comp}.json", | ||
log: | ||
notebook="logs/meta_compare_enrichment/{meta_comp}.ipynb", | ||
params: | ||
desc=lookup(dpath="meta_comparisons/{meta_comp}/desc", within=config), | ||
labels=lookup(dpath="meta_comparisons/{meta_comp}/items/*/label", within=config), | ||
conda: | ||
"../envs/pystats.yaml" | ||
notebook: | ||
"../scripts/compare_enrichment.py.ipynb" | ||
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rule meta_compare_pathways: | ||
input: | ||
expand( | ||
"results/tables/pathways/{model}.pathways.tsv", | ||
model=lookup( | ||
dpath="meta_comparisons/{meta_comp}/items/*/model", within=config | ||
), | ||
), | ||
output: | ||
"results/tables/pathways/meta_compare_{meta_comp}.tsv", | ||
"results/meta_comparison/pathways/{meta_comp}.json", | ||
log: | ||
notebook="logs/meta_compare_pathways/{meta_comp}.ipynb", | ||
params: | ||
desc=lookup(dpath="meta_comparisons/{meta_comp}/desc", within=config), | ||
labels=lookup(dpath="meta_comparisons/{meta_comp}/items/*/label", within=config), | ||
conda: | ||
"../envs/pystats.yaml" | ||
notebook: | ||
"../scripts/compare_pathways.py.ipynb" |
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