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params.yaml
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params.yaml
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# Autogenerated file with ./create-dvc-yaml.py. DO NOT EDIT
WGCNA:
graph:
default_settings:
threshold: 0.6
default_system_settings: {}
stages:
c9orf72_proteomics:
inputs: results/WGCNA/c9orf72_results/adjacency_matrix.feather
outputs: results/WGCNA_graphs/c9orf72_proteomics/graph.gml
settings:
threshold: 0.1
c9orf72_rnaseq:
inputs: results/WGCNA_rnaseq/c9orf72_results/adjacency_matrix.feather
outputs: results/WGCNA_graphs/c9orf72_rnaseq/graph.gml
settings:
threshold: 0.8
fus_proteomics:
inputs: results/WGCNA/fus_results/adjacency_matrix.feather
outputs: results/WGCNA_graphs/fus_proteomics/graph.gml
settings:
threshold: 0.1
fus_rnaseq:
inputs: results/WGCNA_rnaseq/fus_results/adjacency_matrix.feather
outputs: results/WGCNA_graphs/fus_rnaseq/graph.gml
settings: {}
human_proteomics:
inputs: results/WGCNA/human_results/adjacency_matrix.feather
outputs: results/WGCNA_graphs/human_proteomics/graph.gml
settings:
threshold: 0.05
human_rnaseq:
inputs: results/WGCNA_rnaseq/human_results/adjacency_matrix.feather
outputs: results/WGCNA_graphs/human_rnaseq/graph.gml
settings: {}
sod1_proteomics:
inputs: results/WGCNA/sod1_results/adjacency_matrix.feather
outputs: results/WGCNA_graphs/sod1_proteomics/graph.gml
settings:
threshold: 0.1
sod1_rnaseq:
inputs: results/WGCNA_rnaseq/sod1_results/adjacency_matrix.feather
outputs: results/WGCNA_graphs/sod1_rnaseq/graph.gml
settings: {}
tdp43_proteomics:
inputs: results/WGCNA/tdp43_results/adjacency_matrix.feather
outputs: results/WGCNA_graphs/tdp43_proteomics/graph.gml
settings:
threshold: 0.1
tdp43_rnaseq:
inputs: results/WGCNA_rnaseq/tdp43_results/adjacency_matrix.feather
outputs: results/WGCNA_graphs/tdp43_rnaseq/graph.gml
settings: {}
graph_filter:
default_settings:
layout: spring
layout_kwargs: null
max_size: null
min_size: 10
default_system_settings: {}
stages:
c9orf72_proteomics:
inputs: results/WGCNA_graphs/c9orf72_proteomics/graph.gml
outputs: results/WGCNA_graphs/c9orf72_proteomics/
settings: {}
c9orf72_rnaseq:
inputs: results/WGCNA_graphs/c9orf72_rnaseq/graph.gml
outputs: results/WGCNA_graphs/c9orf72_rnaseq/
settings: {}
fus_proteomics:
inputs: results/WGCNA_graphs/fus_proteomics/graph.gml
outputs: results/WGCNA_graphs/fus_proteomics/
settings: {}
fus_rnaseq:
inputs: results/WGCNA_graphs/fus_rnaseq/graph.gml
outputs: results/WGCNA_graphs/fus_rnaseq/
settings: {}
human_proteomics:
inputs: results/WGCNA_graphs/human_proteomics/graph.gml
outputs: results/WGCNA_graphs/human_proteomics/
settings: {}
human_rnaseq:
inputs: results/WGCNA_graphs/human_rnaseq/graph.gml
outputs: results/WGCNA_graphs/human_rnaseq/
settings: {}
sod1_proteomics:
inputs: results/WGCNA_graphs/sod1_proteomics/graph.gml
outputs: results/WGCNA_graphs/sod1_proteomics/
settings: {}
sod1_rnaseq:
inputs: results/WGCNA_graphs/sod1_rnaseq/graph.gml
outputs: results/WGCNA_graphs/sod1_rnaseq/
settings: {}
tdp43_proteomics:
inputs: results/WGCNA_graphs/tdp43_proteomics/graph.gml
outputs: results/WGCNA_graphs/tdp43_proteomics/
settings: {}
tdp43_rnaseq:
inputs: results/WGCNA_graphs/tdp43_rnaseq/graph.gml
outputs: results/WGCNA_graphs/tdp43_rnaseq/
settings: {}
graph_plot:
default_settings: {}
default_system_settings: {}
proteomics:
stages:
c9orf72:
inputs:
celltype_marker: database/celltype_signatures.csv
deg_female: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/deg_digestion/de_tables/only_females-mut_vs_ctrl-strict.csv
deg_full_female: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/deg/only_females/mut_vs_ctrl.csv
deg_full_male: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/deg/only_males/mut_vs_ctrl.csv
deg_male: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/deg_digestion/de_tables/only_males-mut_vs_ctrl-strict.csv
ensemblmapping: database/biomaRt/ensembl_to_symbol_mouse.csv
graph: results/WGCNA_graphs/c9orf72_proteomics/filtered.gml
layout: results/WGCNA_graphs/c9orf72_proteomics/layout.npz
modules: results/WGCNA/c9orf72_results/module_genes.json
uniprotmapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
outputs: results/WGCNA_graphs/c9orf72_proteomics/
settings:
species: Mouse
fus:
inputs:
celltype_marker: database/celltype_signatures.csv
deg_female: datasets/consortium/FUS-mouse/02_organized_data/proteomics/deg_digestion/de_tables/only_females-mut_vs_ctrl-strict.csv
deg_full_female: datasets/consortium/FUS-mouse/02_organized_data/proteomics/deg/only_females/mut_vs_ctrl.csv
deg_full_male: datasets/consortium/FUS-mouse/02_organized_data/proteomics/deg/only_males/mut_vs_ctrl.csv
deg_male: datasets/consortium/FUS-mouse/02_organized_data/proteomics/deg_digestion/de_tables/only_males-mut_vs_ctrl-strict.csv
ensemblmapping: database/biomaRt/ensembl_to_symbol_mouse.csv
graph: results/WGCNA_graphs/fus_proteomics/filtered.gml
layout: results/WGCNA_graphs/fus_proteomics/layout.npz
modules: results/WGCNA/fus_results/module_genes.json
uniprotmapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
outputs: results/WGCNA_graphs/fus_proteomics/
settings:
species: Mouse
human:
inputs:
celltype_marker: database/celltype_signatures.csv
deg_female: datasets/consortium/human-datasets/02_organized_data/proteomics/deg_digestion/de_tables/only_females-mut_vs_ctrl-strict.csv
deg_full_female: datasets/consortium/human-datasets/02_organized_data/proteomics/deg/only_females/mut_vs_ctrl.csv
deg_full_male: datasets/consortium/human-datasets/02_organized_data/proteomics/deg/only_males/mut_vs_ctrl.csv
deg_male: datasets/consortium/human-datasets/02_organized_data/proteomics/deg_digestion/de_tables/only_males-mut_vs_ctrl-strict.csv
ensemblmapping: database/biomaRt/ensembl_to_symbol_human.csv
graph: results/WGCNA_graphs/human_proteomics/filtered.gml
layout: results/WGCNA_graphs/human_proteomics/layout.npz
modules: results/WGCNA/human_results/module_genes.json
uniprotmapping: database/uniprot/uniprot_HUMAN_9606_idmapping_selected.tab.gz
outputs: results/WGCNA_graphs/human_proteomics/
settings:
species: Human
sod1:
inputs:
celltype_marker: database/celltype_signatures.csv
deg_female: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/deg_digestion/de_tables/only_females-mut_vs_ctrl-strict.csv
deg_full_female: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/deg/only_females/mut_vs_ctrl.csv
deg_full_male: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/deg/only_males/mut_vs_ctrl.csv
deg_male: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/deg_digestion/de_tables/only_males-mut_vs_ctrl-strict.csv
ensemblmapping: database/biomaRt/ensembl_to_symbol_mouse.csv
graph: results/WGCNA_graphs/sod1_proteomics/filtered.gml
layout: results/WGCNA_graphs/sod1_proteomics/layout.npz
modules: results/WGCNA/sod1_results/module_genes.json
uniprotmapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
outputs: results/WGCNA_graphs/sod1_proteomics/
settings:
species: Mouse
tdp43:
inputs:
celltype_marker: database/celltype_signatures.csv
deg_female: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/deg_digestion/de_tables/only_females-mut_vs_ctrl-strict.csv
deg_full_female: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/deg/only_females/mut_vs_ctrl.csv
deg_full_male: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/deg/only_males/mut_vs_ctrl.csv
deg_male: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/deg_digestion/de_tables/only_males-mut_vs_ctrl-strict.csv
ensemblmapping: database/biomaRt/ensembl_to_symbol_mouse.csv
graph: results/WGCNA_graphs/tdp43_proteomics/filtered.gml
layout: results/WGCNA_graphs/tdp43_proteomics/layout.npz
modules: results/WGCNA/tdp43_results/module_genes.json
uniprotmapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
outputs: results/WGCNA_graphs/tdp43_proteomics/
settings:
species: Mouse
rnaseq:
stages:
c9orf72:
inputs:
celltype_marker: database/celltype_signatures.csv
deg_female: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/only_females-mut_vs_ctrl-strict.csv
deg_full_female: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/deg/only_females/mut_vs_ctrl.csv
deg_full_male: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/deg/only_males/mut_vs_ctrl.csv
deg_male: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/only_males-mut_vs_ctrl-strict.csv
graph: results/WGCNA_graphs/c9orf72_rnaseq/filtered.gml
layout: results/WGCNA_graphs/c9orf72_rnaseq/layout.npz
modules: results/WGCNA_rnaseq/c9orf72_results/module_genes.json
outputs: results/WGCNA_graphs/c9orf72_rnaseq/
settings:
species: Mouse
fus:
inputs:
celltype_marker: database/celltype_signatures.csv
deg_female: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/only_females-mut_vs_ctrl-strict.csv
deg_full_female: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/deg/only_females/mut_vs_ctrl.csv
deg_full_male: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/deg/only_males/mut_vs_ctrl.csv
deg_male: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/only_males-mut_vs_ctrl-strict.csv
graph: results/WGCNA_graphs/fus_rnaseq/filtered.gml
layout: results/WGCNA_graphs/fus_rnaseq/layout.npz
modules: results/WGCNA_rnaseq/fus_results/module_genes.json
outputs: results/WGCNA_graphs/fus_rnaseq/
settings:
species: Mouse
human:
inputs:
celltype_marker: database/celltype_signatures.csv
deg_female: datasets/consortium/human-datasets/02_organized_data/rnaseq/deg-digestion/de_tables/only_females-mut_vs_ctrl-strict.csv
deg_full_female: datasets/consortium/human-datasets/02_organized_data/rnaseq/deg/only_females/mut_vs_ctrl.csv
deg_full_male: datasets/consortium/human-datasets/02_organized_data/rnaseq/deg/only_males/mut_vs_ctrl.csv
deg_male: datasets/consortium/human-datasets/02_organized_data/rnaseq/deg-digestion/de_tables/only_males-mut_vs_ctrl-strict.csv
graph: results/WGCNA_graphs/human_rnaseq/filtered.gml
layout: results/WGCNA_graphs/human_rnaseq/layout.npz
modules: results/WGCNA_rnaseq/human_results/module_genes.json
outputs: results/WGCNA_graphs/human_rnaseq/
settings:
species: Human
sod1:
inputs:
celltype_marker: database/celltype_signatures.csv
deg_female: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/only_females-mut_vs_ctrl-strict.csv
deg_full_female: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/deg/only_females/mut_vs_ctrl.csv
deg_full_male: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/deg/only_males/mut_vs_ctrl.csv
deg_male: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/only_males-mut_vs_ctrl-strict.csv
graph: results/WGCNA_graphs/sod1_rnaseq/filtered.gml
layout: results/WGCNA_graphs/sod1_rnaseq/layout.npz
modules: results/WGCNA_rnaseq/sod1_results/module_genes.json
outputs: results/WGCNA_graphs/sod1_rnaseq/
settings:
species: Mouse
tdp43:
inputs:
celltype_marker: database/celltype_signatures.csv
deg_female: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/only_females-mut_vs_ctrl-strict.csv
deg_full_female: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/deg/only_females/mut_vs_ctrl.csv
deg_full_male: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/deg/only_males/mut_vs_ctrl.csv
deg_male: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/only_males-mut_vs_ctrl-strict.csv
graph: results/WGCNA_graphs/tdp43_rnaseq/filtered.gml
layout: results/WGCNA_graphs/tdp43_rnaseq/layout.npz
modules: results/WGCNA_rnaseq/tdp43_results/module_genes.json
outputs: results/WGCNA_graphs/tdp43_rnaseq/
settings:
species: Mouse
proteomics:
als_markers_source: ALS_genes_source.csv
literature_dir: results/textmining/csv/literature_top_100_gene.csv
stages:
c9orf72:
annotations: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
de_dir: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/deg
input_file: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
organism: Mus musculus
output_dir: results/WGCNA/c9orf72_results
uniprot_to_ensembl: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
fus:
annotations: datasets/consortium/FUS-mouse/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
de_dir: datasets/consortium/FUS-mouse/02_organized_data/proteomics/deg
input_file: datasets/consortium/FUS-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
organism: Mus musculus
output_dir: results/WGCNA/fus_results
uniprot_to_ensembl: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
human:
annotations: datasets/consortium/human-datasets/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
de_dir: datasets/consortium/human-datasets/02_organized_data/proteomics/deg
input_file: datasets/consortium/human-datasets/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
organism: Homo sapiens
output_dir: results/WGCNA/human_results
uniprot_to_ensembl: database/uniprot/uniprot_HUMAN_9606_idmapping_selected.tab.gz
sod1:
annotations: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
de_dir: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/deg
input_file: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
organism: Mus musculus
output_dir: results/WGCNA/sod1_results
uniprot_to_ensembl: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
tdp43:
annotations: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
de_dir: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/deg
input_file: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
organism: Mus musculus
output_dir: results/WGCNA/tdp43_results
uniprot_to_ensembl: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
rnaseq:
stages:
c9orf72:
MEDissThres: 0.4
annotations: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
de_dir: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/deg
ensembl_to_symbol: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/prefiltering-pca/ENSG_to_symbol.csv
input_file: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_norm_vst.csv
moduleSelectionThreshold: 0.3
organism: Mus musculus
output_dir: results/WGCNA_rnaseq/c9orf72_results
selection:
- ctrl_female
- ctrl_male
- mut_female
- mut_male
softPower: 22
fus:
MEDissThres: 0.5
annotations: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
de_dir: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/deg
ensembl_to_symbol: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/prefiltering-pca/ENSG_to_symbol.csv
input_file: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_norm_vst.csv
moduleSelectionThreshold: 0.3
organism: Mus musculus
output_dir: results/WGCNA_rnaseq/fus_results
selection:
- ctrl_female
- ctrl_male
- mut_female
- mut_male
softPower: 12
human:
MEDissThres: 0
annotations: datasets/consortium/human-datasets/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
de_dir: datasets/consortium/human-datasets/02_organized_data/rnaseq/deg
ensembl_to_symbol: datasets/consortium/human-datasets/02_organized_data/rnaseq/prefiltering-pca/ENSG_to_symbol.csv
input_file: datasets/consortium/human-datasets/02_organized_data/rnaseq/prefiltering-pca/counts_norm_vst.csv
moduleSelectionThreshold: 2
organism: Homo sapiens
output_dir: results/WGCNA_rnaseq/human_results
selection:
- ctrl_female
- ctrl_male
- als_female
- als_male
softPower: 8
sod1:
MEDissThres: 0.4
annotations: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
de_dir: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/deg
ensembl_to_symbol: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/prefiltering-pca/ENSG_to_symbol.csv
input_file: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_norm_vst.csv
moduleSelectionThreshold: 0.5
organism: Mus musculus
output_dir: results/WGCNA_rnaseq/sod1_results
selection:
- ctrl_female
- ctrl_male
- mut_female
- mut_male
softPower: 19
tdp43:
MEDissThres: 0.4
annotations: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
de_dir: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/deg
ensembl_to_symbol: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/prefiltering-pca/ENSG_to_symbol.csv
input_file: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_norm_vst.csv
moduleSelectionThreshold: 0.5
organism: Mus musculus
output_dir: results/WGCNA_rnaseq/tdp43_results
selection:
- ctrl_female
- ctrl_male
- mut_female
- mut_male
softPower: 15
upset:
main_bar_plot_ratio: 0.5
matrix_plot_ratio: 0.5
nintersects: 50
order_by: freq
out_dir: results/WGCNA/upset
png_height: 1080
png_res: 150
png_width: 1920
stages:
c9orf72: results/WGCNA/c9orf72_results/module_genes.json
fus: results/WGCNA/fus_results/module_genes.json
sod1: results/WGCNA/sod1_results/module_genes.json
tdp43: results/WGCNA/tdp43_results/module_genes.json
text_scale: 0.7
integration:
cluster_profiler_compare:
default_settings: {}
default_system_settings: {}
stages:
human_rnaseq:
settings:
absfoldchange_cutoff: 0.29
formula: SEX
function: enrichGO
inputs: results/integration/deg/human_rnaseq.csv
neg_foldchange_cutoff: 1000000
output_directory: results/integration/clusterprofiler/human_rnaseq/
pos_foldchange_cutoff: -1000000
pvalue_cutoff: 0.05
proteomics_sex_model:
settings:
absfoldchange_cutoff: 0.29
formula: SEX + MODEL
function: enrichGO
inputs: results/integration/deg/proteomics.csv
neg_foldchange_cutoff: 1000000
output_directory: results/integration/clusterprofiler/proteomics_sex_model/
pos_foldchange_cutoff: -1000000
pvalue_cutoff: 0.05
splitby:
- SEX
- MODEL
rnaseq_sex_model:
settings:
absfoldchange_cutoff: 0.29
formula: SEX + MODEL
function: enrichGO
inputs: results/integration/deg/rnaseq.csv
neg_foldchange_cutoff: 1000000
output_directory: results/integration/clusterprofiler/rnaseq_sex_model/
pos_foldchange_cutoff: -1000000
pvalue_cutoff: 0.05
splitby:
- SEX
- MODEL
sex_omic_model:
settings:
absfoldchange_cutoff: 0.29
formula: SEX + OMIC + MODEL
function: enrichGO
inputs: results/integration/deg/all_models.csv
neg_foldchange_cutoff: 1000000
output_directory: results/integration/clusterprofiler/sex_omic_model/
pos_foldchange_cutoff: -1000000
pvalue_cutoff: 0.05
splitby: null
cluster_profiler_merge:
default_settings: {}
default_system_settings: {}
stages:
all:
inputs: results/integration/deg/lists/
output: results/integration/deg/all_models.csv
settings:
filter: false
human_rnaseq:
inputs: results/integration/deg/lists/
output: results/integration/deg/human_rnaseq.csv
settings:
filter: MODEL == 'HUMAN' & OMIC == 'rnaseq'
proteomics:
inputs: results/integration/deg/lists/
output: results/integration/deg/proteomics.csv
settings:
filter: OMIC == 'proteomics'
rnaseq:
inputs: results/integration/deg/lists/
output: results/integration/deg/rnaseq.csv
settings:
filter: OMIC == 'rnaseq'
map_de_genes:
default_settings:
species_mapping: human_rat_mouse_protein_gene_link.csv.gz
target: human
default_system_settings: {}
stages:
c9orf72_proteomics_females:
inputs:
de: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/deg/only_females/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/c9orf72_proteomics_females.csv
settings:
datatype: proteomics
species: mouse
c9orf72_proteomics_males:
inputs:
de: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/deg/only_males/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/c9orf72_proteomics_males.csv
settings:
datatype: proteomics
species: mouse
c9orf72_rnaseq_females:
inputs:
de: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/deg/only_females/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/c9orf72_rnaseq_females.csv
settings:
datatype: rnaseq
species: mouse
c9orf72_rnaseq_males:
inputs:
de: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/deg/only_males/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/c9orf72_rnaseq_males.csv
settings:
datatype: rnaseq
species: mouse
fus_proteomics_females:
inputs:
de: datasets/consortium/FUS-mouse/02_organized_data/proteomics/deg/only_females/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/fus_proteomics_females.csv
settings:
datatype: proteomics
species: mouse
fus_proteomics_males:
inputs:
de: datasets/consortium/FUS-mouse/02_organized_data/proteomics/deg/only_males/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/fus_proteomics_males.csv
settings:
datatype: proteomics
species: mouse
fus_rnaseq_females:
inputs:
de: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/deg/only_females/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/fus_rnaseq_females.csv
settings:
datatype: rnaseq
species: mouse
fus_rnaseq_males:
inputs:
de: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/deg/only_males/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/fus_rnaseq_males.csv
settings:
datatype: rnaseq
species: mouse
human_proteomics_females:
inputs:
de: datasets/consortium/human-datasets/02_organized_data/proteomics/deg/only_females/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_HUMAN_9606_idmapping_selected.tab.gz
output: results/integration/deg/lists/human_proteomics_females.csv
settings:
datatype: proteomics
species: human
human_proteomics_males:
inputs:
de: datasets/consortium/human-datasets/02_organized_data/proteomics/deg/only_males/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_HUMAN_9606_idmapping_selected.tab.gz
output: results/integration/deg/lists/human_proteomics_males.csv
settings:
datatype: proteomics
species: human
human_rnaseq_females:
inputs:
de: datasets/consortium/human-datasets/02_organized_data/rnaseq/deg/only_females/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_HUMAN_9606_idmapping_selected.tab.gz
output: results/integration/deg/lists/human_rnaseq_females.csv
settings:
datatype: rnaseq
species: human
human_rnaseq_males:
inputs:
de: datasets/consortium/human-datasets/02_organized_data/rnaseq/deg/only_males/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_HUMAN_9606_idmapping_selected.tab.gz
output: results/integration/deg/lists/human_rnaseq_males.csv
settings:
datatype: rnaseq
species: human
sod1_proteomics_females:
inputs:
de: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/deg/only_females/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/sod1_proteomics_females.csv
settings:
datatype: proteomics
species: mouse
sod1_proteomics_males:
inputs:
de: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/deg/only_males/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/sod1_proteomics_males.csv
settings:
datatype: proteomics
species: mouse
sod1_rnaseq_females:
inputs:
de: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/deg/only_females/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/sod1_rnaseq_females.csv
settings:
datatype: rnaseq
species: mouse
sod1_rnaseq_males:
inputs:
de: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/deg/only_males/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/sod1_rnaseq_males.csv
settings:
datatype: rnaseq
species: mouse
tdp43_proteomics_females:
inputs:
de: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/deg/only_females/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/tdp43_proteomics_females.csv
settings:
datatype: proteomics
species: mouse
tdp43_proteomics_males:
inputs:
de: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/deg/only_males/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/tdp43_proteomics_males.csv
settings:
datatype: proteomics
species: mouse
tdp43_rnaseq_females:
inputs:
de: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/deg/only_females/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/tdp43_rnaseq_females.csv
settings:
datatype: rnaseq
species: mouse
tdp43_rnaseq_males:
inputs:
de: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/deg/only_males/mut_vs_ctrl.csv
mapping: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
output: results/integration/deg/lists/tdp43_rnaseq_males.csv
settings:
datatype: rnaseq
species: mouse
pathway_scores_proteomics:
default_settings:
args: {}
idtype: UNIPROT
methods:
- mlm
- ulm
- wsum
omic: proteomics
default_system_settings: {}
stages:
c9:
inputs:
expression: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
genelists: database/genesets/all_genesets.json.gz
output: results/decoupler/proteomics/c9
settings:
species: mouse
fus:
inputs:
expression: datasets/consortium/FUS-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
genelists: database/genesets/all_genesets.json.gz
output: results/decoupler/proteomics/fus
settings:
species: mouse
human:
inputs:
expression: datasets/consortium/human-datasets/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
genelists: database/genesets/all_genesets.json.gz
output: results/decoupler/proteomics/human
settings:
species: human
sod1:
inputs:
expression: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
genelists: database/genesets/all_genesets.json.gz
output: results/decoupler/proteomics/sod1
settings:
species: mouse
tdp43:
inputs:
expression: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
genelists: database/genesets/all_genesets.json.gz
output: results/decoupler/proteomics/tdp43
settings:
species: mouse
pathway_scores_rnaseq:
default_settings:
args: {}
idtype: ENSEMBL
methods:
- mlm
- ulm
- wsum
omic: rnaseq
default_system_settings: {}
stages:
c9:
inputs:
expression: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_norm_vst.csv
genelists: database/genesets/all_genesets.json.gz
output: results/decoupler/rnaseq/c9
settings:
species: mouse
fus:
inputs:
expression: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_norm_vst.csv
genelists: database/genesets/all_genesets.json.gz
output: results/decoupler/rnaseq/fus
settings:
species: mouse
human:
inputs:
expression: datasets/consortium/human-datasets/02_organized_data/rnaseq/prefiltering-pca/counts_norm_vst.csv
genelists: database/genesets/all_genesets.json.gz
output: results/decoupler/rnaseq/human
settings:
species: human
sod1:
inputs:
expression: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_norm_vst.csv
genelists: database/genesets/all_genesets.json.gz
output: results/decoupler/rnaseq/sod1
settings:
species: mouse
tdp43:
inputs:
expression: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_norm_vst.csv
genelists: database/genesets/all_genesets.json.gz
output: results/decoupler/rnaseq/tdp43
settings:
species: mouse
rnaseq_proteomics_intersection:
default_settings: {}
default_system_settings: {}
stages:
c9:
settings:
output_directory: results/integration/rnaseq_proteomics/C9orf72-mouse/
protein_group_to_proteins: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/organized/protein_group_to_proteins.rds
proteomics_de_results: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/deg/covariate_sex/mut_vs_ctrl.rds
rnaseq_de_results: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/covariate_sex-mut_vs_ctrl-strict_justpval.csv
uniprot_to_ensembl: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
fus:
settings:
output_directory: results/integration/rnaseq_proteomics/FUS-mouse/
protein_group_to_proteins: datasets/consortium/FUS-mouse/02_organized_data/proteomics/organized/protein_group_to_proteins.rds
proteomics_de_results: datasets/consortium/FUS-mouse/02_organized_data/proteomics/deg/covariate_sex/mut_vs_ctrl.rds
rnaseq_de_results: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/covariate_sex-mut_vs_ctrl-strict_justpval.csv
uniprot_to_ensembl: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
human:
settings:
output_directory: results/integration/rnaseq_proteomics/human/
protein_group_to_proteins: datasets/consortium/human-datasets/02_organized_data/proteomics/organized/protein_group_to_proteins.rds
proteomics_de_results: datasets/consortium/human-datasets/02_organized_data/proteomics/deg/covariate_sex/mut_vs_ctrl.rds
rnaseq_de_results: datasets/consortium/human-datasets/02_organized_data/rnaseq/deg-digestion/de_tables/covariate_sex-mut_vs_ctrl-strict_justpval.csv
uniprot_to_ensembl: database/uniprot/uniprot_HUMAN_9606_idmapping_selected.tab.gz
sod1:
settings:
output_directory: results/integration/rnaseq_proteomics/SOD1-mouse/
protein_group_to_proteins: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/organized/protein_group_to_proteins.rds
proteomics_de_results: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/deg/covariate_sex/mut_vs_ctrl.rds
rnaseq_de_results: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/covariate_sex-mut_vs_ctrl-strict_justpval.csv
uniprot_to_ensembl: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
tdp43:
settings:
output_directory: results/integration/rnaseq_proteomics/TDP43-mouse/
protein_group_to_proteins: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/organized/protein_group_to_proteins.rds
proteomics_de_results: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/deg/covariate_sex/mut_vs_ctrl.rds
rnaseq_de_results: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/deg-digestion/de_tables/covariate_sex-mut_vs_ctrl-strict_justpval.csv
uniprot_to_ensembl: database/uniprot/uniprot_MOUSE_10090_idmapping_selected.tab.gz
rnaseq_srna_intersection:
default_settings: {}
default_system_settings: {}
stages:
c9:
settings:
output_directory: results/integration/rnaseq_srna_intersection/C9orf72-mouse
rnaseq_de_digested_dir: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/deg-digestion/
rnaseq_prefiltpca_dir: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/prefiltering-pca/
srna_deg_digestion_dir: datasets/consortium/C9orf72-mouse/02_organized_data/srna/deg-digestion/
fus:
settings:
output_directory: results/integration/rnaseq_srna_intersection/FUS-mouse
rnaseq_de_digested_dir: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/deg-digestion/
rnaseq_prefiltpca_dir: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/prefiltering-pca/
srna_deg_digestion_dir: datasets/consortium/FUS-mouse/02_organized_data/srna/deg-digestion/
human:
settings:
output_directory: results/integration/rnaseq_srna_intersection/human-brain
rnaseq_de_digested_dir: datasets/consortium/human-datasets/02_organized_data/rnaseq/deg-digestion/
rnaseq_prefiltpca_dir: datasets/consortium/human-datasets/02_organized_data/rnaseq/prefiltering-pca/
srna_deg_digestion_dir: datasets/consortium/human-datasets/02_organized_data/srna/deg-digestion/
sod1:
settings:
output_directory: results/integration/rnaseq_srna_intersection/SOD1-mouse
rnaseq_de_digested_dir: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/deg-digestion/
rnaseq_prefiltpca_dir: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/prefiltering-pca/
srna_deg_digestion_dir: datasets/consortium/SOD1-mouse/02_organized_data/srna/deg-digestion/
tdp43:
settings:
output_directory: results/integration/rnaseq_srna_intersection/TDP43-mouse
rnaseq_de_digested_dir: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/deg-digestion/
rnaseq_prefiltpca_dir: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/prefiltering-pca/
srna_deg_digestion_dir: datasets/consortium/TDP43-mouse/02_organized_data/srna/deg-digestion/
mofa_tp2sm:
stages:
sod1:
factor_combinations:
- - 1
- 2
model_training:
seed: 5082
omics:
metabolomics:
annotation_file: datasets/consortium/SOD1-mouse/01_received_data/cohort/sample_annotations.csv
expression_file: datasets/consortium/SOD1-mouse/02_organized_data/metabolomics/prefiltering-pca/normalized_abundance_total_normalized.csv
phosphoproteomics:
annotation_file: datasets/consortium/SOD1-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/SOD1-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
proteomics:
annotation_file: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
srna_mature:
annotation_file: datasets/consortium/SOD1-mouse/02_organized_data/srna/prefiltering_pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/SOD1-mouse/02_organized_data/srna/prefiltering_pca/mature_counts_mat.rds
keep_file: datasets/consortium/SOD1-mouse/02_organized_data/srna/prefiltering_pca/to_keep_mirna_mature.rds
transcriptomics:
annotation_file: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_raw_no_outliers_no_low_genes.csv
organism: Mus musculus
out_dir: results/MOFA/sod1_tp2sm_results
sex_selection:
- all
topN_byVar: null
sod1_reduced:
factor_combinations:
- - 1
- 2
model_training:
seed: 6718
omics:
metabolomics:
annotation_file: datasets/consortium/SOD1-mouse/01_received_data/cohort/sample_annotations.csv
expression_file: datasets/consortium/SOD1-mouse/02_organized_data/metabolomics/prefiltering-pca/normalized_abundance_total_normalized.csv
phosphoproteomics:
annotation_file: datasets/consortium/SOD1-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/SOD1-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
proteomics:
annotation_file: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/SOD1-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
srna_mature:
annotation_file: datasets/consortium/SOD1-mouse/02_organized_data/srna/prefiltering_pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/SOD1-mouse/02_organized_data/srna/prefiltering_pca/mature_counts_mat.rds
keep_file: datasets/consortium/SOD1-mouse/02_organized_data/srna/prefiltering_pca/to_keep_mirna_mature.rds
transcriptomics:
annotation_file: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/SOD1-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_raw_no_outliers_no_low_genes.csv
organism: Mus musculus
out_dir: results/MOFA/sod1_tp2sm_results_reduced
sex_selection:
- all
topN_byVar: 3000
tdp43:
factor_combinations:
- - 1
- 2
model_training:
seed: 1164
omics:
metabolomics:
annotation_file: datasets/consortium/TDP43-mouse/01_received_data/cohort/sample_annotations.csv
expression_file: datasets/consortium/TDP43-mouse/02_organized_data/metabolomics/prefiltering-pca/normalized_abundance_total_normalized.csv
phosphoproteomics:
annotation_file: datasets/consortium/TDP43-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/TDP43-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
proteomics:
annotation_file: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
srna_mature:
annotation_file: datasets/consortium/TDP43-mouse/02_organized_data/srna/prefiltering_pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/TDP43-mouse/02_organized_data/srna/prefiltering_pca/mature_counts_mat.rds
keep_file: datasets/consortium/TDP43-mouse/02_organized_data/srna/prefiltering_pca/to_keep_mirna_mature.rds
transcriptomics:
annotation_file: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_raw_no_outliers_no_low_genes.csv
organism: Mus musculus
out_dir: results/MOFA/tdp43_tp2sm_results
sex_selection:
- all
topN_byVar: null
tdp43_reduced:
factor_combinations:
- - 1
- 2
model_training:
seed: 6953
omics:
metabolomics:
annotation_file: datasets/consortium/TDP43-mouse/01_received_data/cohort/sample_annotations.csv
expression_file: datasets/consortium/TDP43-mouse/02_organized_data/metabolomics/prefiltering-pca/normalized_abundance_total_normalized.csv
phosphoproteomics:
annotation_file: datasets/consortium/TDP43-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/TDP43-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
proteomics:
annotation_file: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/TDP43-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
srna_mature:
annotation_file: datasets/consortium/TDP43-mouse/02_organized_data/srna/prefiltering_pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/TDP43-mouse/02_organized_data/srna/prefiltering_pca/mature_counts_mat.rds
keep_file: datasets/consortium/TDP43-mouse/02_organized_data/srna/prefiltering_pca/to_keep_mirna_mature.rds
transcriptomics:
annotation_file: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/TDP43-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_raw_no_outliers_no_low_genes.csv
organism: Mus musculus
out_dir: results/MOFA/tdp43_tp2sm_results_reduced
sex_selection:
- all
topN_byVar: 3000
mofa_tp2sm_c9:
stages:
c9orf72:
factor_combinations:
- - 1
- 2
model_training:
seed: 7019
omics:
metabolomics:
annotation_file: datasets/consortium/C9orf72-mouse/01_received_data/cohort/sample_annotations.csv
expression_file: datasets/consortium/C9orf72-mouse/02_organized_data/metabolomics/prefiltering-pca/normalized_abundance_total_normalized.csv
sample_mapping: datasets/consortium/C9orf72-mouse/01_received_data/metabolomics/sample_map.tsv
phosphoproteomics:
annotation_file: datasets/consortium/C9orf72-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/C9orf72-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
sample_matching: datasets/consortium/C9orf72-mouse/01_received_data/phosphoproteomics/sample_matching.tsv
proteomics:
annotation_file: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
srna_mature:
annotation_file: datasets/consortium/C9orf72-mouse/02_organized_data/srna/prefiltering_pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/C9orf72-mouse/02_organized_data/srna/prefiltering_pca/mature_counts_mat.rds
keep_file: datasets/consortium/C9orf72-mouse/02_organized_data/srna/prefiltering_pca/to_keep_mirna_mature.rds
transcriptomics:
annotation_file: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_raw_no_outliers_no_low_genes.csv
organism: Mus musculus
out_dir: results/MOFA/c9orf72_tp2sm_results
sex_selection:
- all
topN_byVar: null
c9orf72_reduced_c9:
factor_combinations:
- - 1
- 2
model_training:
seed: 5121
omics:
metabolomics:
annotation_file: datasets/consortium/C9orf72-mouse/01_received_data/cohort/sample_annotations.csv
expression_file: datasets/consortium/C9orf72-mouse/02_organized_data/metabolomics/prefiltering-pca/normalized_abundance_total_normalized.csv
sample_mapping: datasets/consortium/C9orf72-mouse/01_received_data/metabolomics/sample_map.tsv
phosphoproteomics:
annotation_file: datasets/consortium/C9orf72-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/C9orf72-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
sample_matching: datasets/consortium/C9orf72-mouse/01_received_data/phosphoproteomics/sample_matching.tsv
proteomics:
annotation_file: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/C9orf72-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
srna_mature:
annotation_file: datasets/consortium/C9orf72-mouse/02_organized_data/srna/prefiltering_pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/C9orf72-mouse/02_organized_data/srna/prefiltering_pca/mature_counts_mat.rds
keep_file: datasets/consortium/C9orf72-mouse/02_organized_data/srna/prefiltering_pca/to_keep_mirna_mature.rds
transcriptomics:
annotation_file: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/C9orf72-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_raw_no_outliers_no_low_genes.csv
organism: Mus musculus
out_dir: results/MOFA/c9orf72_tp2sm_results_reduced
sex_selection:
- all
topN_byVar: 3000
mofa_tp2sm_fus:
stages:
fus:
factor_combinations:
- - 1
- 2
model_training:
seed: 7404
omics:
metabolomics:
annotation_file: datasets/consortium/FUS-mouse/01_received_data/cohort/sample_annotations.csv
expression_file: datasets/consortium/FUS-mouse/02_organized_data/metabolomics/prefiltering-pca/normalized_abundance_total_normalized.csv
sample_mapping: datasets/consortium/FUS-mouse/01_received_data/metabolomics/sample_map.tsv
phosphoproteomics:
annotation_file: datasets/consortium/FUS-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/FUS-mouse/02_organized_data/phosphoproteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
proteomics:
annotation_file: datasets/consortium/FUS-mouse/02_organized_data/proteomics/prefiltering-pca/cohort_filtered.csv
expression_file: datasets/consortium/FUS-mouse/02_organized_data/proteomics/prefiltering-pca/intensity_mat_filtered_imputed_log2transf_norm.csv
srna_mature:
annotation_file: datasets/consortium/FUS-mouse/02_organized_data/srna/prefiltering_pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/FUS-mouse/02_organized_data/srna/prefiltering_pca/mature_counts_mat.rds
keep_file: datasets/consortium/FUS-mouse/02_organized_data/srna/prefiltering_pca/to_keep_mirna_mature.rds
transcriptomics:
annotation_file: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/prefiltering-pca/cohort_excluded_outliers.csv
expression_file: datasets/consortium/FUS-mouse/02_organized_data/rnaseq/prefiltering-pca/counts_raw_no_outliers_no_low_genes.csv
organism: Mus musculus
out_dir: results/MOFA/fus_tp2sm_results
sex_selection:
- all
topN_byVar: null
fus_reduced:
factor_combinations:
- - 1
- 2
model_training:
seed: 1498
omics: