Files in Gibbons-Lab/mbtools
Provides helper functions for microbiome preprocessing and analysis

.Rbuildignore
.bumpversion.cfg
.gitignore
.travis.yml
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
R/RcppExports.R R/barcodes.R R/convert.R R/counting.R R/files.R R/lineage.R R/logging.R R/mangling.R R/mbtools-package.R R/mock.R R/nanopore.R R/plots.R R/preprocess.R R/qa.R R/refdb.R R/remove_ref.R R/shotgun.R R/sra.R R/testing.R R/util.R R/workflow_dada2.R R/workflow_download.R R/workflow_qa.R R/zzz.R README.md
_pkgdown.yml
docs/LICENSE-text.html
docs/articles/amplicon_sequencing.html
docs/articles/amplicon_sequencing_files/figure-html/unnamed-chunk-11-1.png
docs/articles/amplicon_sequencing_files/figure-html/unnamed-chunk-2-1.png
docs/articles/index.html
docs/articles/mock_example.html
docs/articles/mock_example_files/figure-html/unnamed-chunk-18-1.png
docs/articles/mock_example_files/figure-html/unnamed-chunk-19-1.png
docs/articles/mock_example_files/figure-html/unnamed-chunk-5-1.png
docs/articles/mock_example_files/figure-html/unnamed-chunk-5-2.png
docs/articles/mock_example_files/figure-html/unnamed-chunk-9-1.png
docs/articles/mock_example_files/figure-html/unnamed-chunk-9-2.png
docs/articles/preprocessing.html
docs/articles/qa.html
docs/articles/qa_files/figure-html/unnamed-chunk-4-1.png
docs/articles/qa_files/figure-html/unnamed-chunk-5-1.png
docs/articles/qa_files/figure-html/unnamed-chunk-6-1.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/align_bowtie2.html
docs/reference/align_long_reads.html
docs/reference/align_short_reads.html
docs/reference/annotate_contigs.html
docs/reference/as.matrix.mbquant.html
docs/reference/as_phyloseq.html
docs/reference/association.html
docs/reference/build_lineage.html
docs/reference/combinatorial_association.html
docs/reference/config_align_long.html
docs/reference/config_align_short.html
docs/reference/config_count.html
docs/reference/config_demultiplex.html
docs/reference/config_denoise.html
docs/reference/config_preprocess.html
docs/reference/config_reference.html
docs/reference/config_sra.html
docs/reference/count_transcripts.html
docs/reference/demultiplex.html
docs/reference/denoise.html
docs/reference/discretize.html
docs/reference/download_bacterial_transcripts.html
docs/reference/download_files.html
docs/reference/download_index.html
docs/reference/effective_lengths.html
docs/reference/em_count.html
docs/reference/filter_counts.html
docs/reference/filter_reference.html
docs/reference/find_read_files.html
docs/reference/find_taxa.html
docs/reference/index.html
docs/reference/mbtools.html
docs/reference/merge_transcripts.html
docs/reference/mock_plot.html
docs/reference/mockrobiota.html
docs/reference/mothur_to_dada.html
docs/reference/normalize.html
docs/reference/orlitsky.html
docs/reference/parse_ensembl_id.html
docs/reference/plot_counts.html
docs/reference/plot_entropy.html
docs/reference/plot_lengths.html
docs/reference/plot_qualities.html
docs/reference/plot_taxa.html
docs/reference/preprocess.html
docs/reference/quality_control.html
docs/reference/quality_profile.html
docs/reference/read_bam.html
docs/reference/read_blast.html
docs/reference/read_slimm.html
docs/reference/remove_organism.html
docs/reference/remove_reference.html
docs/reference/run_slimm.html
docs/reference/select.html
docs/reference/silva_build_taxonomy.html
docs/reference/slimm.html
docs/reference/split_barcodes.html
docs/reference/sra_files.html
docs/reference/sra_submission.html
docs/reference/standardize.html
docs/reference/taxa_count.html
docs/reference/taxa_metrics.html
docs/reference/taxa_quants.html
docs/reference/types.html
inst/extdata/example/F3D0_S188_L001_R1_001.fastq.gz
inst/extdata/example/F3D0_S188_L001_R2_001.fastq.gz
inst/extdata/example/F3D1_S189_L001_R1_001.fastq.gz
inst/extdata/example/F3D1_S189_L001_R2_001.fastq.gz
inst/extdata/example/F3D2_S190_L001_R1_001.fastq.gz
inst/extdata/example/F3D2_S190_L001_R2_001.fastq.gz
inst/extdata/example/F3D3_S191_L001_R1_001.fastq.gz
inst/extdata/example/F3D3_S191_L001_R2_001.fastq.gz
inst/extdata/example/HMP_MOCK.v35.fasta
inst/extdata/example/Mock_S280_L001_R1_001.fastq.gz
inst/extdata/example/Mock_S280_L001_R2_001.fastq.gz
inst/extdata/genomes/phiX.fa.gz
man/align_long_reads.Rd man/align_short_reads.Rd man/annotate_contigs.Rd man/as.matrix.mbquant.Rd man/as_phyloseq.Rd man/association.Rd man/build_lineage.Rd man/combinatorial_association.Rd man/config_align_long.Rd man/config_align_short.Rd man/config_count.Rd man/config_demultiplex.Rd man/config_denoise.Rd man/config_preprocess.Rd man/config_reference.Rd man/config_sra.Rd man/count_transcripts.Rd man/demultiplex.Rd man/denoise.Rd man/discretize.Rd man/download_bacterial_transcripts.Rd man/download_files.Rd man/effective_lengths.Rd man/em_count.Rd man/filter_counts.Rd man/filter_reference.Rd man/find_read_files.Rd man/find_taxa.Rd man/mbtools.Rd man/merge_transcripts.Rd man/mock_plot.Rd man/mockrobiota.Rd man/mothur_to_dada.Rd man/normalize.Rd man/orlitsky.Rd man/parse_ensembl_id.Rd man/plot_counts.Rd man/plot_entropy.Rd man/plot_lengths.Rd man/plot_qualities.Rd man/plot_taxa.Rd man/preprocess.Rd man/quality_control.Rd man/quality_profile.Rd man/read_bam.Rd man/read_blast.Rd man/read_slimm.Rd man/remove_reference.Rd man/select.Rd man/silva_build_taxonomy.Rd man/slimm.Rd man/sra_files.Rd man/sra_submission.Rd man/standardize.Rd man/taxa_count.Rd man/taxa_metrics.Rd man/taxa_quants.Rd man/types.Rd man/with_classification.Rd
src/.gitignore
src/Makevars
src/RcppExports.cpp
src/em.cpp
tests/testthat.R tests/testthat/test_barcodes.R tests/testthat/test_convert.R tests/testthat/test_mock.R tests/testthat/test_remove.R vignettes/amplicon_sequencing.Rmd vignettes/preprocessing.Rmd vignettes/qa.Rmd
Gibbons-Lab/mbtools documentation built on March 19, 2019, 8:40 p.m.