Files in bailey-lab/miplicorn
A Framework for Molecular Inversion Probe and Amplicon Analysis
.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug-report.md
.github/ISSUE_TEMPLATE/config.yml
.github/ISSUE_TEMPLATE/feature-request.md
.github/workflows/check-standard.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
.pre-commit-config.yaml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/arrange_natural.R
R/chromosome-map-deprecated.R
R/chromosome-map.R
R/convert.R
R/data-genomes.R
R/dplyr-compatibility.R
R/example.R
R/filter.R
R/label_mutations.R
R/miplicorn-package.R
R/mutation-frequency.R
R/mutation-prevalence.R
R/plot_coverage.R
R/read-deprecated.R
R/read-tbl-classes.R
R/read-tbl.R
R/sysdata.rda
R/themes.R
R/utils-pipe.R
R/utils-tidy-eval.R
R/utils.R
R/zzz.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
data-raw/genome_Pf3D7.R
data-raw/internal_data.R
data/genome_Pf3D7.rda
inst/WORDLIST
inst/extdata/PlasmoDB-53_Pfalciparum3D7.gff
inst/extdata/alternate_AA_table.csv
inst/extdata/coverage_AA_table.csv
inst/extdata/reference_AA_table.csv
man/arrange_natural.Rd
man/chromosome-map.Rd
man/chromosome_map.Rd
man/convert_single.Rd
man/custom_themes.Rd
man/figures/README-usage-1.png
man/figures/README-usage-2.png
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/figures/logo.png
man/filter.Rd
man/filter_fn_factory.Rd
man/genome_Pf3D7.Rd
man/label_mutations.Rd
man/miplicorn-package.Rd
man/miplicorn_example.Rd
man/mutation_frequency.Rd
man/mutation_prevalence.Rd
man/pipe.Rd
man/plot_coverage.Rd
man/plot_mutation_frequency.Rd
man/plot_mutation_prevalence.Rd
man/read-deprecated.Rd
man/read-tbl.Rd
man/tidyeval.Rd
miplicorn.Rproj
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/spelling.R
tests/testthat.R
tests/testthat/_snaps/arrange_natural.md
tests/testthat/_snaps/chromosome-map-deprecated.md
tests/testthat/_snaps/chromosome-map.md
tests/testthat/_snaps/chromosome-map/chromoMap-colours-list.png
tests/testthat/_snaps/chromosome-map/chromoMap-colours-vec.png
tests/testthat/_snaps/chromosome-map/chromoMap-default.png
tests/testthat/_snaps/chromosome-map/chromoMap-no-colour.png
tests/testthat/_snaps/chromosome-map/chromoMap-no-legend.png
tests/testthat/_snaps/chromosome-map/chromoMap-single-colour-list.png
tests/testthat/_snaps/chromosome-map/chromoMap-single-colour-vec.png
tests/testthat/_snaps/chromosome-map/chromoMap-single-colour.png
tests/testthat/_snaps/chromosome-map/chromoMap-single-default.png
tests/testthat/_snaps/chromosome-map/chromoMap-title.png
tests/testthat/_snaps/chromosome-map/karyoploter-arbitrary-column-names.svg
tests/testthat/_snaps/chromosome-map/karyoploter-chrom-color.svg
tests/testthat/_snaps/chromosome-map/karyoploter-chrom-label-size.svg
tests/testthat/_snaps/chromosome-map/karyoploter-default-colours.svg
tests/testthat/_snaps/chromosome-map/karyoploter-default-plot-many-probes.svg
tests/testthat/_snaps/chromosome-map/karyoploter-default-plot-one-probe.svg
tests/testthat/_snaps/chromosome-map/karyoploter-many-colours-vec.svg
tests/testthat/_snaps/chromosome-map/karyoploter-minor-tick-marks.svg
tests/testthat/_snaps/chromosome-map/karyoploter-one-colour-vec.svg
tests/testthat/_snaps/chromosome-map/karyoploter-one-colour.svg
tests/testthat/_snaps/chromosome-map/karyoploter-plot-params.svg
tests/testthat/_snaps/chromosome-map/karyoploter-tick-marks.svg
tests/testthat/_snaps/chromosome-map/karyoploter-title.svg
tests/testthat/_snaps/filter.md
tests/testthat/_snaps/label_mutations.md
tests/testthat/_snaps/mutation-frequency.md
tests/testthat/_snaps/mutation-frequency/autoplot-method-works.svg
tests/testthat/_snaps/mutation-frequency/default-plot-is-informative.svg
tests/testthat/_snaps/mutation-frequency/plot-method-works.svg
tests/testthat/_snaps/mutation-prevalence.md
tests/testthat/_snaps/mutation-prevalence/autoplot-method-works.svg
tests/testthat/_snaps/mutation-prevalence/default-plot-is-informative.svg
tests/testthat/_snaps/mutation-prevalence/plot-method-works.svg
tests/testthat/_snaps/plot_coverage.md
tests/testthat/_snaps/plot_coverage/can-add-ggplot2-layers.svg
tests/testthat/_snaps/plot_coverage/default-plot-is-informative.svg
tests/testthat/_snaps/read-deprecated.md
tests/testthat/_snaps/read-tbl-classes.md
tests/testthat/_snaps/read-tbl.md
tests/testthat/_snaps/themes/default-theme.svg
tests/testthat/_snaps/themes/rainbow-theme.svg
tests/testthat/_snaps/themes/theme-miplicorn.svg
tests/testthat/_snaps/themes/theme-rainbow.svg
tests/testthat/empty-file
tests/testthat/haplotype_test.csv
tests/testthat/preserve-sample-id.csv
tests/testthat/small.csv
tests/testthat/test-arrange_natural.R
tests/testthat/test-chromosome-map-deprecated.R
tests/testthat/test-chromosome-map.R
tests/testthat/test-convert.R
tests/testthat/test-example.R
tests/testthat/test-filter.R
tests/testthat/test-label_mutations.R
tests/testthat/test-mutation-frequency.R
tests/testthat/test-mutation-prevalence.R
tests/testthat/test-plot_coverage.R
tests/testthat/test-read-deprecated.R
tests/testthat/test-read-tbl-classes.R
tests/testthat/test-read-tbl.R
tests/testthat/test-themes.R
vignettes/.gitignore
vignettes/faq.Rmd
vignettes/large-files.Rmd
vignettes/miplicorn.Rmd
