├── .gitignore ├── 2018_ASM_Workshop.Rproj ├── README.md ├── analysis ├── 16S_analysis.Rmd ├── R_introduction-ANSWERS.Rmd ├── R_introduction-ANSWERS.html ├── R_introduction.Rmd ├── R_introduction.html ├── dada2_tutorial.Rmd ├── dada2_tutorial.html ├── media │ ├── ASVs_ASM.pdf │ ├── DADA2_Logo_640.png │ ├── OTUs_vs_ASVs_sm.png │ ├── amplicon_schematic.png │ ├── phyloseq-classes.png │ ├── phyloseq-summary.png │ └── pseudo_480.png └── mini-tutorial.Rmd └── data ├── 16S_data.RDS ├── 16S_mapping.txt ├── fastqs ├── 806rcbc288_R1.fastq.gz ├── 806rcbc288_R2.fastq.gz ├── 806rcbc289_R1.fastq.gz ├── 806rcbc289_R2.fastq.gz ├── 806rcbc290_R1.fastq.gz ├── 806rcbc290_R2.fastq.gz ├── 806rcbc291_R1.fastq.gz ├── 806rcbc291_R2.fastq.gz ├── 806rcbc292_R1.fastq.gz ├── 806rcbc292_R2.fastq.gz ├── 806rcbc293_R1.fastq.gz ├── 806rcbc293_R2.fastq.gz ├── 806rcbc294_R1.fastq.gz ├── 806rcbc294_R2.fastq.gz ├── 806rcbc295_R1.fastq.gz ├── 806rcbc295_R2.fastq.gz ├── 806rcbc296_R1.fastq.gz ├── 806rcbc296_R2.fastq.gz ├── 806rcbc297_R1.fastq.gz ├── 806rcbc297_R2.fastq.gz ├── 806rcbc298_R1.fastq.gz ├── 806rcbc298_R2.fastq.gz ├── 806rcbc299_R1.fastq.gz ├── 806rcbc299_R2.fastq.gz ├── 806rcbc300_R1.fastq.gz ├── 806rcbc300_R2.fastq.gz ├── 806rcbc301_R1.fastq.gz ├── 806rcbc301_R2.fastq.gz ├── 806rcbc302_R1.fastq.gz ├── 806rcbc302_R2.fastq.gz ├── 806rcbc303_R1.fastq.gz └── 806rcbc303_R2.fastq.gz ├── mapping_wnv_antibiotics.txt ├── ps0.wnv_antibiotics.gg.RDS ├── ps0.wnv_antibiotics.silva.RDS ├── rdp_train_set_16.fa.gz └── taxa.rds /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/.gitignore -------------------------------------------------------------------------------- /2018_ASM_Workshop.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/2018_ASM_Workshop.Rproj -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/README.md -------------------------------------------------------------------------------- /analysis/16S_analysis.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/16S_analysis.Rmd -------------------------------------------------------------------------------- /analysis/R_introduction-ANSWERS.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/R_introduction-ANSWERS.Rmd -------------------------------------------------------------------------------- /analysis/R_introduction-ANSWERS.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/R_introduction-ANSWERS.html -------------------------------------------------------------------------------- /analysis/R_introduction.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/R_introduction.Rmd -------------------------------------------------------------------------------- /analysis/R_introduction.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/R_introduction.html -------------------------------------------------------------------------------- /analysis/dada2_tutorial.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/dada2_tutorial.Rmd -------------------------------------------------------------------------------- /analysis/dada2_tutorial.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/dada2_tutorial.html -------------------------------------------------------------------------------- /analysis/media/ASVs_ASM.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/media/ASVs_ASM.pdf -------------------------------------------------------------------------------- /analysis/media/DADA2_Logo_640.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/media/DADA2_Logo_640.png -------------------------------------------------------------------------------- /analysis/media/OTUs_vs_ASVs_sm.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/media/OTUs_vs_ASVs_sm.png -------------------------------------------------------------------------------- /analysis/media/amplicon_schematic.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/media/amplicon_schematic.png -------------------------------------------------------------------------------- /analysis/media/phyloseq-classes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/media/phyloseq-classes.png -------------------------------------------------------------------------------- /analysis/media/phyloseq-summary.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/media/phyloseq-summary.png -------------------------------------------------------------------------------- /analysis/media/pseudo_480.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/media/pseudo_480.png -------------------------------------------------------------------------------- /analysis/mini-tutorial.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/analysis/mini-tutorial.Rmd -------------------------------------------------------------------------------- /data/16S_data.RDS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/16S_data.RDS -------------------------------------------------------------------------------- /data/16S_mapping.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/16S_mapping.txt -------------------------------------------------------------------------------- /data/fastqs/806rcbc288_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc288_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc288_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc288_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc289_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc289_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc289_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc289_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc290_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc290_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc290_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc290_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc291_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc291_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc291_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc291_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc292_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc292_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc292_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc292_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc293_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc293_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc293_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc293_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc294_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc294_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc294_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc294_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc295_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc295_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc295_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc295_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc296_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc296_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc296_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc296_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc297_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc297_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc297_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc297_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc298_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc298_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc298_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc298_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc299_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc299_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc299_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc299_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc300_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc300_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc300_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc300_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc301_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc301_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc301_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc301_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc302_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc302_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc302_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc302_R2.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc303_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc303_R1.fastq.gz -------------------------------------------------------------------------------- /data/fastqs/806rcbc303_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/fastqs/806rcbc303_R2.fastq.gz -------------------------------------------------------------------------------- /data/mapping_wnv_antibiotics.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/mapping_wnv_antibiotics.txt -------------------------------------------------------------------------------- /data/ps0.wnv_antibiotics.gg.RDS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/ps0.wnv_antibiotics.gg.RDS -------------------------------------------------------------------------------- /data/ps0.wnv_antibiotics.silva.RDS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/ps0.wnv_antibiotics.silva.RDS -------------------------------------------------------------------------------- /data/rdp_train_set_16.fa.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/rdp_train_set_16.fa.gz -------------------------------------------------------------------------------- /data/taxa.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shandley/Microbiome-Analysis-Using-R/HEAD/data/taxa.rds --------------------------------------------------------------------------------