papaa@0.1.9_PI3K_OG_model_tutorial 1.0
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Run on GalaxyPanCancer Aberrant Pathway Activity Analysis: PI3K example
Associated Tutorial
This workflows is part of the tutorial PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis, available in the GTN
Thanks to...
Tutorial Author(s): Vijay, Daniel Blankenberg
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| CCLE_DepMap_18Q1_maf_20180207.txt | CCLE_DepMap_18Q1_maf_20180207.txt | n/a |
|
| CCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv | CCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv | n/a |
|
| GDSC_CCLE_common_mut_cnv_binary.tsv.gz | GDSC_CCLE_common_mut_cnv_binary.tsv.gz | n/a |
|
| GDSC_EXP_CCLE_converted_name.tsv.gz | GDSC_EXP_CCLE_converted_name.tsv.gz | n/a |
|
| GSE69822_pi3k_sign.txt | GSE69822_pi3k_sign.txt | n/a |
|
| GSE69822_pi3k_trans.csv | GSE69822_pi3k_trans.csv | n/a |
|
| ccle_rnaseq_genes_rpkm_20180929_mod.tsv.gz | ccle_rnaseq_genes_rpkm_20180929_mod.tsv.gz | n/a |
|
| compounds_of_interest.txt | compounds_of_interest.txt | n/a |
|
| copy_number_gain_status.tsv | copy_number_gain_status.tsv | n/a |
|
| copy_number_loss_status.tsv | copy_number_loss_status.tsv | n/a |
|
| cosmic_cancer_classification.tsv | cosmic_cancer_classification.tsv | n/a |
|
| gdsc1_ccle_pharm_fitted_dose_data.txt | gdsc1_ccle_pharm_fitted_dose_data.txt | n/a |
|
| gdsc2_ccle_pharm_fitted_dose_data.txt | gdsc2_ccle_pharm_fitted_dose_data.txt | n/a |
|
| mc3.v0.2.8.PUBLIC.maf | mc3.v0.2.8.PUBLIC.maf | n/a |
|
| mutation_burden_freeze.tsv | mutation_burden_freeze.tsv | n/a |
|
| pancan_mutation_freeze.tsv | pancan_mutation_freeze.tsv | n/a |
|
| pancan_rnaseq_freeze.tsv | pancan_rnaseq_freeze.tsv | n/a |
|
| path_rtk_ras_pi3k_genes.txt | path_rtk_ras_pi3k_genes.txt | n/a |
|
| sample_freeze.tsv | sample_freeze.tsv | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 19 | PAPAA: PanCancer classifier | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_classifier/pancancer_classifier/0.1.9 |
| 20 | PAPAA: PanCancer within disease analysis | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_within_disease_analysis/pancancer_within_disease_analysis/0.1.9 |
| 21 | PAPAA: PanCancer apply weights | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_apply_weights/pancancer_apply_weights/0.1.9 |
| 22 | PAPAA: PanCancer external sample status prediction | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_external_sample_status_prediction/pancancer_external_sample_status_prediction/0.1.9 |
| 23 | PAPAA: PanCancer compare within models | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_compare_within_models/pancancer_compare_within_models/0.1.9 |
| 24 | PAPAA: PanCancer visualize decisions | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_visualize_decisions/pancancer_visualize_decisions/0.1.9 |
| 25 | PAPAA: PanCancer alternative genes pathwaymapper | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_alternative_genes_pathwaymapper/pancancer_alternative_genes_pathwaymapper/0.1.9 |
| 26 | PAPAA: PanCancer map mutation class | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_map_mutation_class/pancancer_map_mutation_class/0.1.9 |
| 27 | PAPAA: PanCancer pathway count heatmaps | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_pathway_count_heatmaps/pancancer_pathway_count_heatmaps/0.1.9 |
| 28 | PAPAA: PanCancer targene summary figures | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_summary_figures/pancancer_targene_summary_figures/0.1.9 |
| 29 | PAPAA: PanCancer targene cell line predictions | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_cell_line_predictions/pancancer_targene_cell_line_predictions/0.1.9 |
| 30 | PAPAA: PanCancer targene pharmacology | toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_pharmacology/pancancer_targene_pharmacology/0.1.9 |
Version History
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Creators and Submitter
Views: 1198 Downloads: 174 Runs: 0
Created: 2nd Jun 2025 at 11:00
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