.gitignore
LICENSE
README.md
pyproject.toml
requirements.txt
requirements_legacy.txt
setup.py
conda_env/environment.yml
examples/methylation.csv
examples/methylation_for_quantification.csv
examples/miRNA.tsv
examples/miRNA_for_quantification.tsv
examples/multiple_inputs_1.xlsx
examples/multiple_inputs_2.xlsx
examples/single_input_bulk.xlsx
examples/single_input_genes.xlsx
examples/single_input_transcripts.xlsx
examples/draw_KEGG_2024-12-12_3_inputs/genes_per_cell.xlsx
examples/draw_KEGG_2024-12-12_3_inputs/ko04932_Non-alcoholic_fatty_liver_disease.eps
examples/draw_KEGG_2024-12-12_3_inputs/mmu04932_Non-alcoholic_fatty_liver_disease.pdf
examples/draw_KEGG_2024-12-12_3_inputs/pathways_per_gene_input1.xlsx
examples/draw_KEGG_2024-12-12_3_inputs/pathways_per_gene_input2.xlsx
examples/draw_KEGG_2024-12-12_3_inputs/pathways_per_gene_input3.xlsx
examples/draw_KEGG_2024-12-12_bulk/genes_per_cell.xlsx
examples/draw_KEGG_2024-12-12_bulk/genes_per_cell_input_format.xlsx
examples/draw_KEGG_2024-12-12_bulk/mmu04932_Non-alcoholic_fatty_liver_disease.eps
examples/draw_KEGG_2024-12-12_bulk/mmu04932_Non-alcoholic_fatty_liver_disease.pdf
examples/draw_KEGG_2024-12-12_bulk/mmu04932_Non-alcoholic_fatty_liver_disease_colorbar.eps
examples/draw_KEGG_2024-12-12_bulk/pathways_per_gene.xlsx
examples/draw_KEGG_2024-12-12_genes/genes_per_cell.xlsx
examples/draw_KEGG_2024-12-12_genes/genes_per_cell_input_format.xlsx
examples/draw_KEGG_2024-12-12_genes/mmu04932_Non-alcoholic_fatty_liver_disease.eps
examples/draw_KEGG_2024-12-12_genes/mmu04932_Non-alcoholic_fatty_liver_disease.pdf
examples/draw_KEGG_2024-12-12_genes/mmu04932_Non-alcoholic_fatty_liver_disease_colorbar.eps
examples/draw_KEGG_2024-12-12_genes/pathways_per_gene.xlsx
examples/draw_KEGG_2024-12-12_genes_compounds/genes_per_cell.xlsx
examples/draw_KEGG_2024-12-12_genes_compounds/genes_per_cell_input_format.xlsx
examples/draw_KEGG_2024-12-12_genes_compounds/mmu04932_Non-alcoholic_fatty_liver_disease.eps
examples/draw_KEGG_2024-12-12_genes_compounds/mmu04932_Non-alcoholic_fatty_liver_disease.pdf
examples/draw_KEGG_2024-12-12_genes_compounds/mmu04932_Non-alcoholic_fatty_liver_disease_colorbar.eps
examples/draw_KEGG_2024-12-12_genes_compounds/pathways_per_gene.xlsx
examples/draw_KEGG_2024-12-12_methylation/genes_per_cell.xlsx
examples/draw_KEGG_2024-12-12_methylation/genes_per_cell_input_format.xlsx
examples/draw_KEGG_2024-12-12_methylation/mmu04932_Non-alcoholic_fatty_liver_disease.eps
examples/draw_KEGG_2024-12-12_methylation/mmu04932_Non-alcoholic_fatty_liver_disease.pdf
examples/draw_KEGG_2024-12-12_methylation/pathways_per_gene.xlsx
examples/draw_KEGG_2024-12-12_methylation_and_miRNA/genes_per_cell.xlsx
examples/draw_KEGG_2024-12-12_methylation_and_miRNA/genes_per_cell_input_format.xlsx
examples/draw_KEGG_2024-12-12_methylation_and_miRNA/mmu04932_Non-alcoholic_fatty_liver_disease.eps
examples/draw_KEGG_2024-12-12_methylation_and_miRNA/mmu04932_Non-alcoholic_fatty_liver_disease.pdf
examples/draw_KEGG_2024-12-12_methylation_and_miRNA/pathways_per_gene.xlsx
examples/draw_KEGG_2024-12-12_methylation_quantification/cgs_per_gene.xlsx
examples/draw_KEGG_2024-12-12_methylation_quantification/genes_per_cell.xlsx
examples/draw_KEGG_2024-12-12_methylation_quantification/genes_per_cell_input_format.xlsx
examples/draw_KEGG_2024-12-12_methylation_quantification/mmu04932_Non-alcoholic_fatty_liver_disease.eps
examples/draw_KEGG_2024-12-12_methylation_quantification/mmu04932_Non-alcoholic_fatty_liver_disease.pdf
examples/draw_KEGG_2024-12-12_methylation_quantification/mmu04932_Non-alcoholic_fatty_liver_disease_colorbar.eps
examples/draw_KEGG_2024-12-12_methylation_quantification/mmu04932_per_gene_hist.eps
examples/draw_KEGG_2024-12-12_methylation_quantification/mmu04932_per_gene_hist_grouped.eps
examples/draw_KEGG_2024-12-12_methylation_quantification/pathways_per_gene.xlsx
examples/draw_KEGG_2024-12-12_methylation_quantification_probe_correction/cgs_per_gene.xlsx
examples/draw_KEGG_2024-12-12_methylation_quantification_probe_correction/genes_per_cell.xlsx
examples/draw_KEGG_2024-12-12_methylation_quantification_probe_correction/genes_per_cell_input_format.xlsx
examples/draw_KEGG_2024-12-12_methylation_quantification_probe_correction/mmu04932_Non-alcoholic_fatty_liver_disease.eps
examples/draw_KEGG_2024-12-12_methylation_quantification_probe_correction/mmu04932_Non-alcoholic_fatty_liver_disease.pdf
examples/draw_KEGG_2024-12-12_methylation_quantification_probe_correction/mmu04932_Non-alcoholic_fatty_liver_disease_colorbar.eps
examples/draw_KEGG_2024-12-12_methylation_quantification_probe_correction/mmu04932_per_gene_hist.eps
examples/draw_KEGG_2024-12-12_methylation_quantification_probe_correction/mmu04932_per_gene_hist_grouped.eps
examples/draw_KEGG_2024-12-12_methylation_quantification_probe_correction/pathways_per_gene.xlsx
examples/draw_KEGG_2024-12-12_miRNA_quantification/genes_per_cell.xlsx
examples/draw_KEGG_2024-12-12_miRNA_quantification/genes_per_cell_input_format.xlsx
examples/draw_KEGG_2024-12-12_miRNA_quantification/miRNAs_per_gene.xlsx
examples/draw_KEGG_2024-12-12_miRNA_quantification/mmu04932_Non-alcoholic_fatty_liver_disease.eps
examples/draw_KEGG_2024-12-12_miRNA_quantification/mmu04932_Non-alcoholic_fatty_liver_disease.pdf
examples/draw_KEGG_2024-12-12_miRNA_quantification/mmu04932_Non-alcoholic_fatty_liver_disease_colorbar.eps
examples/draw_KEGG_2024-12-12_miRNA_quantification/mmu04932_per_gene_hist.eps
examples/draw_KEGG_2024-12-12_miRNA_quantification/mmu04932_per_gene_hist_grouped.eps
examples/draw_KEGG_2024-12-12_miRNA_quantification/pathways_per_gene.xlsx
examples/draw_KEGG_2024-12-12_transcripts/genes_per_cell.xlsx
examples/draw_KEGG_2024-12-12_transcripts/genes_per_cell_input_format.xlsx
examples/draw_KEGG_2024-12-12_transcripts/mmu04932_Non-alcoholic_fatty_liver_disease.eps
examples/draw_KEGG_2024-12-12_transcripts/mmu04932_Non-alcoholic_fatty_liver_disease.pdf
examples/draw_KEGG_2024-12-12_transcripts/mmu04932_Non-alcoholic_fatty_liver_disease_colorbar.eps
examples/draw_KEGG_2024-12-12_transcripts/pathways_per_gene.xlsx
examples/my_folder_name_with_extension/genes_per_cell.xlsx
examples/my_folder_name_with_extension/genes_per_cell_input_format.xlsx
examples/my_folder_name_with_extension/mmu04932_Non-alcoholic_fatty_liver_disease.eps
examples/my_folder_name_with_extension/mmu04932_Non-alcoholic_fatty_liver_disease.pdf
examples/my_folder_name_with_extension/mmu04932_Non-alcoholic_fatty_liver_disease_colorbar.eps
examples/my_folder_name_with_extension/pathways_per_gene.xlsx
src/__init__.py
src/metaKEGG/__init__.py
src/metaKEGG/cli.py
src/metaKEGG/config.py
src/metaKEGG.egg-info/PKG-INFO
src/metaKEGG.egg-info/SOURCES.txt
src/metaKEGG.egg-info/dependency_links.txt
src/metaKEGG.egg-info/requires.txt
src/metaKEGG.egg-info/top_level.txt
src/metaKEGG/helpers/__init__.py
src/metaKEGG/helpers/helpfunctions.py
src/metaKEGG/modules/__init__.py
src/metaKEGG/modules/colorscale.py
src/metaKEGG/modules/drawing_functions.py
src/metaKEGG/modules/pipeline.py
src/metaKEGG/modules/pipeline_async.py
tests/__init__.py
tests/test_config.py
tests/test_pipeline.py
tests/test_pipeline_async.py