Files in kpj/dce

Pathway Enrichment Based on Differential Causal Effects

.Rbuildignore

.github/linters/.python-black

.github/linters/.snakefmt.toml

.github/workflows/check-bioc.yml

.github/workflows/linter.yml

.github/workflows/pkgdown.yaml

.gitignore

.lintr

DESCRIPTION

NAMESPACE

NEWS.md R/data.R R/data_simulation.R R/graph_utils.R R/main.R R/pathway_databases.R R/plotting.R R/solver_glm.R R/solver_mle.R R/utils.R README.md

_pkgdown.yml

data-raw/df_pathway_statistics.R data-raw/logo.R

data/df_pathway_statistics.rda

inst/CITATION

inst/scripts/crispr_benchmark/README.md

inst/scripts/crispr_benchmark/config/config.yaml

inst/scripts/crispr_benchmark/config/params.csv

inst/scripts/crispr_benchmark/lsf.yaml

inst/scripts/crispr_benchmark/run_cluster.sh

inst/scripts/crispr_benchmark/workflow/Snakefile

inst/scripts/crispr_benchmark/workflow/envs/stack.yaml

inst/scripts/crispr_benchmark/workflow/scripts/additional_statistics.py

inst/scripts/crispr_benchmark/workflow/scripts/aggregated_statistics.R inst/scripts/crispr_benchmark/workflow/scripts/analyze_single_perturbed_gene.R

inst/scripts/crispr_benchmark/workflow/scripts/compare_performance.py

inst/scripts/crispr_benchmark/workflow/scripts/compute_dces.R

inst/scripts/crispr_benchmark/workflow/scripts/compute_performance.py

inst/scripts/crispr_benchmark/workflow/scripts/pathway_statistics.R

inst/scripts/crispr_benchmark/workflow/scripts/plot_performance.py

inst/scripts/crispr_benchmark/workflow/scripts/retrieve_pathways.R inst/scripts/gtex_validation/README.md

inst/scripts/gtex_validation/config/config.yaml

inst/scripts/gtex_validation/run_cluster.sh

inst/scripts/gtex_validation/workflow/Snakefile

inst/scripts/gtex_validation/workflow/envs/stack.yaml

inst/scripts/gtex_validation/workflow/scripts/compare_tissues.R inst/scripts/gtex_validation/workflow/scripts/explore_data.R inst/scripts/gtex_validation/workflow/scripts/get_statistics.R inst/scripts/gtex_validation/workflow/scripts/plot_dce.R inst/scripts/gtex_validation/workflow/scripts/plot_results.R inst/scripts/gtex_validation/workflow/scripts/prepare_all_datasets.R inst/scripts/gtex_validation/workflow/scripts/prepare_dataset.R inst/scripts/gtex_validation/workflow/scripts/prepare_expressions.R inst/scripts/gtex_validation/workflow/scripts/prepare_gene_encodings.R inst/scripts/ovarian_cancer/README.md

inst/scripts/ovarian_cancer/RetrieveCovariates.ipynb

inst/scripts/ovarian_cancer/analysis.R

inst/scripts/ovarian_cancer/covariates.csv

inst/scripts/ovarian_cancer/hsa04210.csv

inst/scripts/ovarian_cancer/hsa04350.csv

inst/scripts/synthetic_benchmark/README.md

inst/scripts/synthetic_benchmark/config/config.yaml

inst/scripts/synthetic_benchmark/lsf.yaml

inst/scripts/synthetic_benchmark/resources/pathways.rds

inst/scripts/synthetic_benchmark/run_benchmark.sh

inst/scripts/synthetic_benchmark/workflow/Snakefile

inst/scripts/synthetic_benchmark/workflow/envs/stack.yaml

inst/scripts/synthetic_benchmark/workflow/scripts/Carnival.R inst/scripts/synthetic_benchmark/workflow/scripts/DGE.R inst/scripts/synthetic_benchmark/workflow/scripts/FastGGM.R inst/scripts/synthetic_benchmark/workflow/scripts/LDGM.R

inst/scripts/synthetic_benchmark/workflow/scripts/LDGM/L1GeneralCompositeGradientAccelerated.m

inst/scripts/synthetic_benchmark/workflow/scripts/LDGM/LogisticLoss.m

inst/scripts/synthetic_benchmark/workflow/scripts/LDGM/differential_graph.m

inst/scripts/synthetic_benchmark/workflow/scripts/LDGM/myProcessOptions.m

inst/scripts/synthetic_benchmark/workflow/scripts/LDGM/test_differential_graph.m

inst/scripts/synthetic_benchmark/workflow/scripts/execute_causaldag.py

inst/scripts/synthetic_benchmark/workflow/scripts/helper_functions.R inst/scripts/synthetic_benchmark/workflow/scripts/main.R inst/scripts/synthetic_benchmark/workflow/scripts/models.R inst/scripts/synthetic_benchmark/workflow/scripts/performance_measures.R inst/scripts/synthetic_benchmark/workflow/scripts/plotting.R inst/scripts/synthetic_benchmark/workflow/scripts/reconstruction.R inst/scripts/synthetic_benchmark/workflow/scripts/sub.R inst/scripts/tcga_pipeline/README.md

inst/scripts/tcga_pipeline/config/config.yaml

inst/scripts/tcga_pipeline/workflow/Snakefile

inst/scripts/tcga_pipeline/workflow/envs/stack.yaml

inst/scripts/tcga_pipeline/workflow/notebooks/ProcessTCGAData.ipynb

inst/scripts/tcga_pipeline/workflow/scripts/compute_dce.R

inst/scripts/tcga_pipeline/workflow/scripts/drug_discovery.py

inst/scripts/tcga_pipeline/workflow/scripts/kegg_download.R inst/scripts/tcga_pipeline/workflow/scripts/summarize_results.R inst/scripts/tcga_pipeline/workflow/scripts/tcga_download.R inst/scripts/tcga_pipeline/workflow/scripts/visualize.R man/as.data.frame.dce.Rd man/as_adjmat.Rd man/create_random_DAG.Rd man/dce-methods.Rd man/dce_nb.Rd man/df_pathway_statistics.Rd man/estimate_latent_count.Rd

man/figures/logo.png

man/g2dag.Rd man/get_pathway_info.Rd man/get_pathways.Rd man/get_prediction_counts.Rd man/graph2df.Rd man/graph_union.Rd man/pcor.Rd man/permutation_test.Rd man/plot.dce.Rd man/plot_network.Rd man/propagate_gene_edges.Rd man/resample_edge_weights.Rd man/rlm_dce.Rd man/simulate_data-methods.Rd man/summary.rlm_dce.Rd man/topologically_ordering.Rd man/trueEffects.Rd tests/testthat.R tests/testthat/test-dce.R tests/testthat/test-deconfounding.R tests/testthat/test-graph_utils.R tests/testthat/test-ideas.R tests/testthat/test-plotting.R tests/testthat/test-simulation.R

vignettes/bibliography.bib

vignettes/dce.Rmd vignettes/pathway_databases.Rmd

kpj/dce documentation built on Oct. 29, 2022, 1:40 a.m.