Files in microsud/chkMocks
Compare Mock Community Samples in Microbiome Sequencing Studies
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/assignTaxonomyCustomMock.R
R/checkZymoBiomics.R
R/compare2theorectical.R
R/data.R
R/plotZymoDefault.R
README.md
_pkgdown.yml
chkMocks.Rproj
data-raw/Karstens2019TestData.Rmd
data-raw/ZymoBiomicsGut.csv
data-raw/ZymoBiomicsGutTaxonomy.csv
data-raw/listContaminants.csv
data/ZymoBiomics.rda
data/ZymoBiomicsFasta.rda
data/ZymoBiomicsGut.rda
data/ZymoBiomicsGutPseq.rda
data/ZymoBiomicsGutTrainingSet.rda
data/ZymoBiomicsPseq.rda
data/ZymoExamplePseq.rda
data/ZymoTrainingSet.rda
docs/404.html
docs/LICENSE-text.html
docs/articles/01_Introduction.html
docs/articles/01_Introduction_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/01_Introduction_files/figure-html/unnamed-chunk-6-1.png
docs/articles/01_Introduction_files/figure-html/unnamed-chunk-7-1.png
docs/articles/01_Introduction_files/figure-html/unnamed-chunk-8-1.png
docs/articles/02_CreateCustomDatabase.html
docs/articles/02_CreateCustomDatabase_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/CreateCustomDatabase.html
docs/articles/CreateCustomDatabase_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/Introduction.html
docs/articles/Introduction_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/Introduction_files/figure-html/unnamed-chunk-5-1.png
docs/articles/Introduction_files/figure-html/unnamed-chunk-6-1.png
docs/articles/aIntroduction.html
docs/articles/aIntroduction_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/aIntroduction_files/figure-html/unnamed-chunk-10-1.png
docs/articles/aIntroduction_files/figure-html/unnamed-chunk-11-1.png
docs/articles/aIntroduction_files/figure-html/unnamed-chunk-7-1.png
docs/articles/aIntroduction_files/figure-html/unnamed-chunk-8-1.png
docs/articles/aIntroduction_files/figure-html/unnamed-chunk-9-1.png
docs/articles/aIntroduction_files/header-attrs-2.10/header-attrs.js
docs/articles/aIntroduction_files/header-attrs-2.8/header-attrs.js
docs/articles/bCreateCustomDatabase.html
docs/articles/bCreateCustomDatabase_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/bCreateCustomDatabase_files/header-attrs-2.10/header-attrs.js
docs/articles/bCreateCustomDatabase_files/header-attrs-2.8/header-attrs.js
docs/articles/cExampleCustomMocks.html
docs/articles/cExampleCustomMocks_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/cExampleCustomMocks_files/figure-html/plot-training-1.png
docs/articles/cExampleCustomMocks_files/figure-html/th-gen-1.png
docs/articles/cExampleCustomMocks_files/figure-html/th-heatmap-1.png
docs/articles/cExampleCustomMocks_files/figure-html/viz-cor-1-1.png
docs/articles/cExampleCustomMocks_files/figure-html/viz-cor-2-1.png
docs/articles/cExampleCustomMocks_files/figure-html/viz-cor-3-1.png
docs/articles/cExampleCustomMocks_files/header-attrs-2.10/header-attrs.js
docs/articles/cExampleCustomMocks_files/header-attrs-2.8/header-attrs.js
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/ZymoBiomics.html
docs/reference/ZymoBiomicsFasta.html
docs/reference/ZymoBiomicsGut.html
docs/reference/ZymoBiomicsGutPseq.html
docs/reference/ZymoBiomicsGutTrainingSet.html
docs/reference/ZymoBiomicsPseq.html
docs/reference/ZymoExamplePseq.html
docs/reference/ZymoTrainingSet.html
docs/reference/assignTaxonomyCustomMock.html
docs/reference/checkZymoBiomics.html
docs/reference/compare2theorectical.html
docs/reference/index.html
docs/reference/plotZymoDefault-1.png
docs/reference/plotZymoDefault.html
docs/sitemap.xml
inst/extdata/MIBPhylotypes.fasta
inst/extdata/MIBTrainingSet.rds
inst/extdata/TaxonomyMIBMocks.csv
inst/extdata/TheoreticalCompositionMIBMocks.csv
inst/extdata/ZymoBiomicsAll.fasta
inst/extdata/ZymoDb.fasta
inst/extdata/ps.mib.rds
inst/extras/ZymoDb
inst/extras/ssrRNAs/Bacillus_subtilis_16S_170923.fasta
inst/extras/ssrRNAs/Cryptococcus_neoformans_18S_170924.fasta
inst/extras/ssrRNAs/Cryptococcus_neoformans_Mitochondria_ssrRNA.fasta
inst/extras/ssrRNAs/Enterococcus_faecalis_16S_170923.fasta
inst/extras/ssrRNAs/Escherichia_coli_16S_170923.fasta
inst/extras/ssrRNAs/Lactobacillus_fermentum_16S_170924.fasta
inst/extras/ssrRNAs/Listeria_monocytogenes_16S_170923.fasta
inst/extras/ssrRNAs/Pseudomonas_aeruginosa_16S_170923.fasta
inst/extras/ssrRNAs/Saccharomyces_cerevisiae_18S_170924.fasta
inst/extras/ssrRNAs/Saccharomyces_cerevisiae_mitochondria_ssrRNA.fasta
inst/extras/ssrRNAs/Salmonella_enterica_16S_170923.fasta
inst/extras/ssrRNAs/Staphylococcus_aureus_16S_170923.fasta
inst/extras/ssrRNAs/ZymoBiomicsAll.fasta
inst/extras/ssrRNAs/ZymoBiomicsAllBAcFungi.txt
inst/extras/ssrRNAs/ZymoBiomicsAllOrginal.fasta
man/ZymoBiomics.Rd
man/ZymoBiomicsFasta.Rd
man/ZymoBiomicsGut.Rd
man/ZymoBiomicsGutPseq.Rd
man/ZymoBiomicsGutTrainingSet.Rd
man/ZymoBiomicsPseq.Rd
man/ZymoExamplePseq.Rd
man/ZymoTrainingSet.Rd
man/assignTaxonomyCustomMock.Rd
man/checkZymoBiomics.Rd
man/compare2theorectical.Rd
man/plotZymoDefault.Rd
tests/testthat.R
tests/testthat/test-checkZymoBiomics.R
vignettes/.gitignore
vignettes/aIntroduction.Rmd
vignettes/bCreateCustomDatabase.Rmd
vignettes/cExampleCustomMocks.Rmd
