Files in ShixiangWang/sigminer
Capture Genomic Variation Signatures using Non-Negative Matrix Factorization

.Rbuildignore
.gitignore
.travis.yml
CRAN-RELEASE
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md R/class.R R/cnv_helper.R R/data.R R/draw_series.R R/get_series.R R/hello.R R/prepare_series.R R/read_series.R R/sig_correlation.R R/sigminer.R R/signature_series.R R/test.R R/utils-pipe.R R/zzz.R README.Rmd README.md
appveyor.yml
codecov.yml
data/centromeres.hg19.rda
data/centromeres.hg38.rda
data/chromsize.hg19.rda
data/chromsize.hg38.rda
docs/LICENSE-text.html
docs/LICENSE.html
docs/README.knit.html
docs/README.utf8.html
docs/articles/index.html
docs/articles/sigminer.html
docs/articles/sigminer_files/figure-html/unnamed-chunk-10-1.png
docs/articles/sigminer_files/figure-html/unnamed-chunk-7-1.png
docs/articles/sigminer_files/figure-html/unnamed-chunk-9-1.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/CopyNumber-class.html
docs/reference/GenomicVariation-class.html
docs/reference/MAF-class.html
docs/reference/centromeres.hg19.html
docs/reference/centromeres.hg38.html
docs/reference/chromsize.hg19.html
docs/reference/chromsize.hg38.html
docs/reference/draw_cn_components.html
docs/reference/draw_cn_distribution.html
docs/reference/draw_cn_features.html
docs/reference/draw_sig_activity.html
docs/reference/draw_sig_corrplot.html
docs/reference/draw_sig_profile.html
docs/reference/draw_subtypes_comparison.html
docs/reference/figures/logo.png
docs/reference/get_ArmLocation.html
docs/reference/get_LengthFraction.html
docs/reference/get_cnlist.html
docs/reference/get_cnsummary_sample.html
docs/reference/get_components.html
docs/reference/get_features.html
docs/reference/get_matrix.html
docs/reference/hello.html
docs/reference/index.html
docs/reference/pipe.html
docs/reference/prepare_copynumber.html
docs/reference/prepare_maf.html
docs/reference/read_copynumber.html
docs/reference/read_maf.html
docs/reference/read_variation.html
docs/reference/sig_assign_samples.html
docs/reference/sig_estimate.html
docs/reference/sig_extract.html
docs/reference/sig_get_activity.html
docs/reference/sig_get_correlation.html
docs/reference/sig_get_similarity.html
docs/reference/sig_prepare.html
docs/reference/sig_summarize_subtypes.html
docs/reference/sigminer.html
docs/reference/subset.CopyNumber.html
docs/reference/test_run_components.html
inst/extdata/blood_normal.segtab.txt
inst/extdata/example_cn_list.RData
inst/extdata/metastatic_tumor.segtab.txt
inst/extdata/solid_tumor.segtab.txt
inst/extdata/toy_cn.RData
inst/extdata/toy_cn_components.RData
inst/extdata/toy_cn_features.RData
inst/extdata/toy_cnlist.RData
inst/extdata/toy_copynumber.RData
inst/extdata/toy_copynumber_prepare.RData
inst/extdata/toy_copynumber_signature.RData
inst/extdata/toy_segTab.RData
inst/figures/array2.png
inst/figures/barchart.png
inst/figures/sigminer.png
inst/test/develop.R inst/test/test.R inst/test/use_hexsticker.R man/CopyNumber-class.Rd man/GenomicVariation-class.Rd man/MAF-class.Rd man/centromeres.hg19.Rd man/centromeres.hg38.Rd man/chromsize.hg19.Rd man/chromsize.hg38.Rd man/draw_cn_components.Rd man/draw_cn_distribution.Rd man/draw_cn_features.Rd man/draw_features_corrplot.Rd man/draw_sig_activity.Rd man/draw_sig_corrplot.Rd man/draw_sig_enrichment.Rd man/draw_sig_profile.Rd man/draw_subtypes_comparison.Rd
man/figures/logo.png
man/filter_enrichment.Rd man/get_ArmLocation.Rd man/get_LengthFraction.Rd man/get_adj_p.Rd man/get_cnlist.Rd man/get_cnsummary_sample.Rd man/get_components.Rd man/get_features.Rd man/get_matrix.Rd man/hello.Rd man/pipe.Rd man/prepare_copynumber.Rd man/prepare_maf.Rd man/read_copynumber.Rd man/read_maf.Rd man/read_variation.Rd man/sig_assign_samples.Rd man/sig_estimate.Rd man/sig_extract.Rd man/sig_get_activity.Rd man/sig_get_correlation.Rd man/sig_get_similarity.Rd man/sig_group_enrichment.Rd man/sig_prepare.Rd man/sig_summarize_correlation.Rd man/sig_summarize_subtypes.Rd man/sig_tidy_correlation.Rd man/sigminer.Rd man/subset.CopyNumber.Rd man/test_run_components.Rd
sigminer.Rproj
tests/testthat.R tests/testthat/test-get_series.R tests/testthat/test-prepare_series.R tests/testthat/test-reading_data.R tests/testthat/test-sig_analysis_series.R
vignettes/.gitignore
vignettes/sigminer.Rmd
ShixiangWang/sigminer documentation built on July 12, 2019, 12:08 p.m.