├── 10X_Visium_samples ├── UMI_annotator.py ├── Visium.R ├── Visium_pipeline.sh ├── output │ ├── CRC_16.visium.raw_matrix.genus.csv │ ├── CRC_16.visium.raw_matrix.validate.csv │ ├── OSCC_2.visium.raw_matrix.genus.csv │ └── OSCC_2.visium.raw_matrix.validate.csv └── validate_and_count.py ├── LICENSE ├── README.md ├── cell_culture_samples ├── DE.r ├── INVADEseq.py ├── cell_culture_16s_pipeline.sh ├── cell_culture_Seurat.r ├── cell_culture_samples_GEX_pipeline.sh ├── merge_metadata.py ├── metadata_dedup.py └── output │ ├── HCT_116_gex_16s_mix_dedup.csv │ └── HT_29_gex_16s_mix_dedup.csv └── patient_samples ├── DE.r ├── INVADEseq.py ├── merge_metadata.py ├── metadata_dedup.py ├── out └── headneck_gex_16s_mix_dedup_updated.csv ├── patient_samples_16s_pipeline.sh ├── patient_samples_GEX_pipeline.sh └── patient_samples_Seurat.r /10X_Visium_samples/UMI_annotator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/10X_Visium_samples/UMI_annotator.py -------------------------------------------------------------------------------- /10X_Visium_samples/Visium.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/10X_Visium_samples/Visium.R -------------------------------------------------------------------------------- /10X_Visium_samples/Visium_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/10X_Visium_samples/Visium_pipeline.sh -------------------------------------------------------------------------------- /10X_Visium_samples/output/CRC_16.visium.raw_matrix.genus.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/10X_Visium_samples/output/CRC_16.visium.raw_matrix.genus.csv -------------------------------------------------------------------------------- /10X_Visium_samples/output/CRC_16.visium.raw_matrix.validate.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/10X_Visium_samples/output/CRC_16.visium.raw_matrix.validate.csv -------------------------------------------------------------------------------- /10X_Visium_samples/output/OSCC_2.visium.raw_matrix.genus.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/10X_Visium_samples/output/OSCC_2.visium.raw_matrix.genus.csv -------------------------------------------------------------------------------- /10X_Visium_samples/output/OSCC_2.visium.raw_matrix.validate.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/10X_Visium_samples/output/OSCC_2.visium.raw_matrix.validate.csv -------------------------------------------------------------------------------- /10X_Visium_samples/validate_and_count.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/10X_Visium_samples/validate_and_count.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/README.md -------------------------------------------------------------------------------- /cell_culture_samples/DE.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/cell_culture_samples/DE.r -------------------------------------------------------------------------------- /cell_culture_samples/INVADEseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/cell_culture_samples/INVADEseq.py -------------------------------------------------------------------------------- /cell_culture_samples/cell_culture_16s_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/cell_culture_samples/cell_culture_16s_pipeline.sh -------------------------------------------------------------------------------- /cell_culture_samples/cell_culture_Seurat.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/cell_culture_samples/cell_culture_Seurat.r -------------------------------------------------------------------------------- /cell_culture_samples/cell_culture_samples_GEX_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/cell_culture_samples/cell_culture_samples_GEX_pipeline.sh -------------------------------------------------------------------------------- /cell_culture_samples/merge_metadata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/cell_culture_samples/merge_metadata.py -------------------------------------------------------------------------------- /cell_culture_samples/metadata_dedup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/cell_culture_samples/metadata_dedup.py -------------------------------------------------------------------------------- /cell_culture_samples/output/HCT_116_gex_16s_mix_dedup.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/cell_culture_samples/output/HCT_116_gex_16s_mix_dedup.csv -------------------------------------------------------------------------------- /cell_culture_samples/output/HT_29_gex_16s_mix_dedup.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/cell_culture_samples/output/HT_29_gex_16s_mix_dedup.csv -------------------------------------------------------------------------------- /patient_samples/DE.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/patient_samples/DE.r -------------------------------------------------------------------------------- /patient_samples/INVADEseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/patient_samples/INVADEseq.py -------------------------------------------------------------------------------- /patient_samples/merge_metadata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/patient_samples/merge_metadata.py -------------------------------------------------------------------------------- /patient_samples/metadata_dedup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/patient_samples/metadata_dedup.py -------------------------------------------------------------------------------- /patient_samples/out/headneck_gex_16s_mix_dedup_updated.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/patient_samples/out/headneck_gex_16s_mix_dedup_updated.csv -------------------------------------------------------------------------------- /patient_samples/patient_samples_16s_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/patient_samples/patient_samples_16s_pipeline.sh -------------------------------------------------------------------------------- /patient_samples/patient_samples_GEX_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/patient_samples/patient_samples_GEX_pipeline.sh -------------------------------------------------------------------------------- /patient_samples/patient_samples_Seurat.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022/HEAD/patient_samples/patient_samples_Seurat.r --------------------------------------------------------------------------------