├── .gitignore ├── IBD_2_subtypes_example ├── input_data │ ├── NIHMS1510763-supplement-Dataset_1.xlsx │ ├── NIHMS1510763-supplement-Dataset_2.xlsx │ ├── NIHMS1510763-supplement-Dataset_6.xlsx │ ├── enzyme_ko.txt │ ├── metabolism_expr.csv │ ├── metabolism_meta.csv │ ├── mg.expr.csv │ ├── mg.meta.csv │ └── name_map.csv ├── result │ ├── IBD.cpd.mpse.rds │ ├── IBD.gene.mpse.rds │ ├── IBD_2_subtypes_gene_ORA.pdf │ ├── IBD_2_subtypes_in_metabolism_ORA.pdf │ ├── cpd-ora.rds │ ├── figure2.pdf │ ├── figure2.png │ ├── ko-ora.rds │ └── module-ko-ora.rds └── script │ ├── IBD_2_subtypes_online.R │ ├── process.metabolism.r │ └── process.metagenome.r ├── LICENSE ├── Phyllostachys_heterocycla_example ├── input_data │ ├── annot_data │ │ ├── Phe_GO_annotation.txt │ │ ├── Phe_TF_list.txt │ │ └── regulation_from_motif_CE_Phe.txt │ ├── counts.txt │ └── group_info.txt ├── result │ ├── figure3.pdf │ └── figure3.png └── script │ └── Phyllostachys_heterocycla_example.R ├── README.Rmd ├── README.md ├── ko00240.xml ├── ko00330.xml ├── single_cell_example ├── input_data │ ├── cell_marker_db │ │ └── c8.all.v2023.1.Hs.symbols.gmt │ └── filtered_gene_bc_matrices │ │ └── hg19 │ │ ├── barcodes.tsv │ │ ├── genes.tsv │ │ └── matrix.mtx ├── result │ ├── figure4-cp.pdf │ ├── figure4.pdf │ └── figure4.png └── script │ └── pbmc_single_cell_example.R └── tables ├── d.rds ├── table-1.R └── table-1.png /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/clusterProfiler_protocol/HEAD/.gitignore -------------------------------------------------------------------------------- /IBD_2_subtypes_example/input_data/NIHMS1510763-supplement-Dataset_1.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/YuLab-SMU/clusterProfiler_protocol/HEAD/IBD_2_subtypes_example/input_data/NIHMS1510763-supplement-Dataset_1.xlsx 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