Files in tobiasgf/lulu
Post Clustering Curation of Amplicon Data for Reliable Biodiversity Metrics
.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
Example_data/README.md
Example_data/centroids_test.txt
Example_data/otutable_test.txt
Files_LULU_manuscript/.DS_Store
Files_LULU_manuscript/CLI scripts/.DS_Store
Files_LULU_manuscript/CLI scripts/Alfa_CROP95.sh
Files_LULU_manuscript/CLI scripts/Alfa_CROP97.sh
Files_LULU_manuscript/CLI scripts/Alfa_CROP98.sh
Files_LULU_manuscript/CLI scripts/Alfa_DADA2_vsearch.sh
Files_LULU_manuscript/CLI scripts/Alfa_concatenate_and_dereplicate_fasta.sh
Files_LULU_manuscript/CLI scripts/Alfa_concatenate_single_samples_fastq_DADA2.sh
Files_LULU_manuscript/CLI scripts/Alfa_demultiplex_universal.sh
Files_LULU_manuscript/CLI scripts/Alfa_matchlists.sh
Files_LULU_manuscript/CLI scripts/Alfa_merge_all_pairs.sh
Files_LULU_manuscript/CLI scripts/Alfa_swarm.sh
Files_LULU_manuscript/CLI scripts/Alfa_vsearch.sh
Files_LULU_manuscript/CLI scripts/Alfa_vsearch_dbotu.sh
Files_LULU_manuscript/CLI scripts/DADA2_demultiplex_tail_trim.sh
Files_LULU_manuscript/CLI scripts/OTU_contingency_table_simple.py
Files_LULU_manuscript/CLI scripts/rename.pl
Files_LULU_manuscript/Data files/.DS_Store
Files_LULU_manuscript/Data files/DADA2_tags_R1A.list
Files_LULU_manuscript/Data files/DADA2_tags_R1B.list
Files_LULU_manuscript/Data files/DADA2_tags_R2A.list
Files_LULU_manuscript/Data files/DADA2_tags_R2B.list
Files_LULU_manuscript/Data files/DADA2_tags_R3A.list
Files_LULU_manuscript/Data files/DADA2_tags_R3B.list
Files_LULU_manuscript/Data files/Table_plants_2014_cleaned.txt
Files_LULU_manuscript/Data files/batchfile.list
Files_LULU_manuscript/Data files/batchfileDADA2.list
Files_LULU_manuscript/Data files/tags_R1A.list
Files_LULU_manuscript/Data files/tags_R1B.list
Files_LULU_manuscript/Data files/tags_R2A.list
Files_LULU_manuscript/Data files/tags_R2B.list
Files_LULU_manuscript/Data files/tags_R3A.list
Files_LULU_manuscript/Data files/tags_R3B.list
Files_LULU_manuscript/README.md
Files_LULU_manuscript/R_markdown files/.DS_Store
Files_LULU_manuscript/R_markdown files/A_Preparation_of_sequences.Rmd
Files_LULU_manuscript/R_markdown files/B_clustering_with_VSEARCH_SWARM_CROP.Rmd
Files_LULU_manuscript/R_markdown files/C_Processing_with_DADA2.Rmd
Files_LULU_manuscript/R_markdown files/D_Taxonomic_filtering.Rmd
Files_LULU_manuscript/R_markdown files/E_LULU_processing.Rmd
Files_LULU_manuscript/R_markdown files/F_Calculating_table_statistics.Rmd
Files_LULU_manuscript/R_markdown files/G_Producing_Figure1.Rmd
Files_LULU_manuscript/R_markdown files/H_Producing_supplementary_figures_1_7.Rmd
Files_LULU_manuscript/R_markdown files/I_GenBank_coverage.Rmd
Files_LULU_manuscript/R_markdown files/J_Dbotu3_onestep_clustering.Rmd
Files_LULU_manuscript/R_markdown files/K_Benchmarking_dbotu3_curation_and_singleton_culling.Rmd
Files_LULU_manuscript/R_markdown files/L_Producing_supplementary_figures_8_16.Rmd
Files_LULU_manuscript/R_markdown files/M_Producing_supplementary_tables.Rmd
Files_LULU_manuscript/R_markdown files/N_Producing_supplementary_figures_17_32.Rmd
Files_LULU_manuscript/R_markdown files/O_Calculating_plotwise__taxonomic_composition_statistics.Rmd
Files_LULU_manuscript/R_markdown files/X_Notes_on_setup.Rmd
LICENSE
NAMESPACE
R/.DS_Store
R/Functions.R
README.md
data/.DS_Store
data/xxx.rda
lulu.Rproj
man/lulu.Rd
