Files in piyalkarum/rCNV
Detect Copy Number Variants from SNPs Data
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/codecov.yml
.github/workflows/test-coverage.yaml
.gitignore
CRAN-SUBMISSION
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/.DS_Store
R/RcppExports.R
R/TMM_normalz.R
R/allele_tests.R
R/bias.det.R
R/cpp_calls.R
R/data.R
R/detect.R
R/exportVCF.R
R/post_detect.R
R/raw_process.R
R/sim.als.R
R/statistics.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
cran-comments.md
data/.DS_Store
data/ADnorm.rda
data/ADtable.rda
data/alleleINF.rda
docs/.nojekyll
docs/404.html
docs/LICENSE.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/Z2.1.svg
docs/articles/Z2.2.svg
docs/articles/chi2.1.svg
docs/articles/chi2.2.svg
docs/articles/dev.plot2.png
docs/articles/dup.plot.parrotfish.png
docs/articles/get.miss.jpeg
docs/articles/h.zygosity.png
docs/articles/index.html
docs/articles/rCNV.html
docs/articles/rCNV_files/figure-html/unnamed-chunk-24-1.png
docs/articles/relatedness.png
docs/articles/workflow2.png
docs/authors.html
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.3.1/bootstrap.min.css
docs/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
docs/deps/clipboard.js-2.0.11/clipboard.min.js
docs/deps/data-deps.txt
docs/deps/font-awesome-6.4.2/css/all.css
docs/deps/font-awesome-6.4.2/css/all.min.css
docs/deps/font-awesome-6.4.2/css/v4-shims.css
docs/deps/font-awesome-6.4.2/css/v4-shims.min.css
docs/deps/font-awesome-6.4.2/webfonts/fa-brands-400.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-brands-400.woff2
docs/deps/font-awesome-6.4.2/webfonts/fa-regular-400.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-regular-400.woff2
docs/deps/font-awesome-6.4.2/webfonts/fa-solid-900.ttf
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docs/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2
docs/deps/headroom-0.11.0/headroom.min.js
docs/deps/headroom-0.11.0/jQuery.headroom.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/deps/search-1.0.0/autocomplete.jquery.min.js
docs/deps/search-1.0.0/fuse.min.js
docs/deps/search-1.0.0/mark.min.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/katex-auto.js
docs/lightswitch.js
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/ADnorm.html
docs/reference/ADtable.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/Rplot004.png
docs/reference/Rplot005.png
docs/reference/Rplot006.png
docs/reference/Rplot007.png
docs/reference/Rplot008.png
docs/reference/Rplot009.png
docs/reference/Rplot010.png
docs/reference/Rplot011.png
docs/reference/Rplot012.png
docs/reference/ad.correct.html
docs/reference/allele.freq.html
docs/reference/allele.info.html
docs/reference/alleleINF-1.png
docs/reference/alleleINF.html
docs/reference/cnv-1.png
docs/reference/cnv.html
docs/reference/cpm.normal-1.png
docs/reference/cpm.normal.html
docs/reference/depthVsSample.html
docs/reference/dup.plot-1.png
docs/reference/dup.plot.html
docs/reference/dup.validate.html
docs/reference/dupGet-1.png
docs/reference/dupGet.html
docs/reference/exportVCF.html
docs/reference/figures/dup.plot.parrotfish.png
docs/reference/figures/dupPlot.png
docs/reference/figures/logo.png
docs/reference/get.miss-1.png
docs/reference/get.miss.html
docs/reference/gt.format.html
docs/reference/h.zygosity.html
docs/reference/hetTgen.html
docs/reference/index.html
docs/reference/maf.html
docs/reference/norm.fact.html
docs/reference/power.bias.html
docs/reference/readVCF.html
docs/reference/relatedness-1.png
docs/reference/relatedness.html
docs/reference/sig.hets-1.png
docs/reference/sig.hets.html
docs/reference/sim.als.html
docs/reference/vcf.stat-1.png
docs/reference/vcf.stat-10.png
docs/reference/vcf.stat-11.png
docs/reference/vcf.stat-12.png
docs/reference/vcf.stat-2.png
docs/reference/vcf.stat-3.png
docs/reference/vcf.stat-4.png
docs/reference/vcf.stat-5.png
docs/reference/vcf.stat-6.png
docs/reference/vcf.stat-7.png
docs/reference/vcf.stat-8.png
docs/reference/vcf.stat-9.png
docs/reference/vcf.stat.html
docs/reference/vst-1.png
docs/reference/vst-2.png
docs/reference/vst.html
docs/reference/vstPermutation-1.png
docs/reference/vstPermutation-2.png
docs/reference/vstPermutation-3.png
docs/reference/vstPermutation.html
docs/search.json
docs/sitemap.xml
dupPlot.png
inst/CITATION
inst/example.raw.vcf.gz
man/ADnorm.Rd
man/ADtable.Rd
man/ad.correct.Rd
man/allele.freq.Rd
man/allele.info.Rd
man/alleleINF.Rd
man/cnv.Rd
man/cpm.normal.Rd
man/depthVsSample.Rd
man/dup.plot.Rd
man/dup.validate.Rd
man/dupGet.Rd
man/exportVCF.Rd
man/figures/dup.plot.parrotfish.png
man/figures/dupPlot.png
man/figures/logo.png
man/get.miss.Rd
man/gt.format.Rd
man/h.zygosity.Rd
man/hetTgen.Rd
man/maf.Rd
man/norm.fact.Rd
man/power.bias.Rd
man/readVCF.Rd
man/relatedness.Rd
man/sig.hets.Rd
man/sim.als.Rd
man/vcf.stat.Rd
man/vst.Rd
man/vstPermutation.Rd
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
rCNV.Rproj
src/RcppExports.cpp
src/RcppExports.o
src/cpp_scripts.cpp
src/cpp_scripts.o
src/rCNV.so
testDATA/Parrotfish_sequenceReads.vcf.gz
testDATA/for_pub/data/Ag_AD.corr.40plus40.rds
testDATA/for_pub/data/Ag_AD.nor.corr.40plus40.rds
testDATA/for_pub/data/PA_ADto_CorrNor_outlRem.rds
testDATA/for_pub/data/PA_AI_outlRem.rds
testDATA/for_pub/data/lobster_AD.corr.outRem.rds
testDATA/for_pub/data/lobster_AD.nor.corr.outRem.rds
testDATA/for_pub/data/salmon_AD.corr.outRem.rds
testDATA/for_pub/data/salmon_AI.nor.corr.outRem.rds
testDATA/for_pub/data/sprucestatsscaffold.rds
testDATA/for_pub/scr/analyses_in_text.R
testDATA/for_pub/scr/bises_in_seq_simulation.R
testDATA/for_pub/scr/sims_for_MS.R
testDATA/lobster_vstDat.rds
tests/testthat.R
tests/testthat/Rplots.pdf
tests/testthat/test-ad.R
tests/testthat/test-allele.R
tests/testthat/test-allele_tests.R
tests/testthat/test-cpm.R
tests/testthat/test-depthVsSample.R
tests/testthat/test-dupGet.R
tests/testthat/test-maf.R
tests/testthat/test-readVCF.R
tests/testthat/test-sim.R
tests/testthat/test-vcf.R
vignettes/.gitignore
vignettes/Z2.1.svg
vignettes/Z2.2.svg
vignettes/chi2.1.svg
vignettes/chi2.2.svg
vignettes/dev.plot2.png
vignettes/devPlot.png
vignettes/dup.plot.parrotfish.png
vignettes/dupPlot.png
vignettes/eq.Z.png
vignettes/eq.chi.svg
vignettes/eq.svg
vignettes/eq2.svg
vignettes/get.miss.jpeg
vignettes/get.miss.png
vignettes/h.zygosity.png
vignettes/logo.png
vignettes/rCNV.Rmd
vignettes/relatedness.png
vignettes/workflow1.png
vignettes/workflow2.png
