├── .dockerignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── GCT.R ├── data.R ├── deprecated.R ├── io.R ├── math.R └── utils.R ├── README.md ├── data ├── cdesc_char.RData ├── ds.RData ├── gene_set.RData └── kd_gct.RData ├── docker ├── Dockerfile └── nginx.conf ├── docs ├── Makefile ├── build │ ├── doctrees │ │ ├── available_modules.doctree │ │ ├── build.doctree │ │ ├── citing.doctree │ │ ├── contributing.doctree │ │ ├── data.doctree │ │ ├── environment.pickle │ │ ├── faq.doctree │ │ ├── index.doctree │ │ ├── io.doctree │ │ ├── licenses.doctree │ │ └── utils.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _sources │ │ ├── available_modules.txt │ │ ├── build.txt │ │ ├── citing.txt │ │ ├── contributing.txt │ │ ├── data.txt │ │ ├── faq.txt │ │ ├── index.txt │ │ ├── io.txt │ │ ├── licenses.txt │ │ └── utils.txt │ │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── basic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── fonts │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ └── fontawesome-webfont.woff │ │ ├── jquery-1.11.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── available_modules.html │ │ ├── build.html │ │ ├── citing.html │ │ ├── contributing.html │ │ ├── data.html │ │ ├── faq.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── io.html │ │ ├── licenses.html │ │ ├── objects.inv │ │ ├── search.html │ │ ├── searchindex.js │ │ └── utils.html └── source │ ├── available_modules.rst │ ├── build.rst │ ├── citing.rst │ ├── conf.py │ ├── contributing.rst │ ├── data.rst │ ├── faq.rst │ ├── index.rst │ ├── io.rst │ ├── licenses.rst │ └── utils.rst ├── inst ├── extdata │ ├── example.lxb │ ├── lm_epsilon_n978.grp │ ├── lm_probes.gmx │ ├── modzs_n25x50.gct │ ├── modzs_n25x50.gctx │ └── query_up.gmt └── script │ └── data.txt ├── install_cmapR.R ├── man ├── GCT-class.Rd ├── GCT.Rd ├── align_matrices.Rd ├── annotate_gct.Rd ├── append_dim.Rd ├── cdesc_char.Rd ├── check_colnames.Rd ├── check_dups.Rd ├── distil.Rd ├── ds.Rd ├── extract_gct.Rd ├── fix_datatypes.Rd ├── gene_set.Rd ├── ids.Rd ├── is.wholenumber.Rd ├── kd_gct.Rd ├── lxb2mat.Rd ├── mat.Rd ├── melt_gct.Rd ├── merge_gct.Rd ├── merge_with_precedence.Rd ├── meta.Rd ├── na_pad_matrix.Rd ├── parse_gctx.Rd ├── parse_gmt.Rd ├── parse_gmx.Rd ├── parse_grp.Rd ├── process_ids.Rd ├── rank_gct.Rd ├── read_gctx_ids.Rd ├── read_gctx_meta.Rd ├── robust_zscore.Rd ├── subset_gct.Rd ├── subset_to_ids.Rd ├── threshold.Rd ├── transpose_gct.Rd ├── update_gctx.Rd ├── write_gct.Rd ├── write_gctx.Rd ├── write_gctx_meta.Rd ├── write_gmt.Rd ├── write_grp.Rd └── write_tbl.Rd ├── tests ├── testthat.R └── testthat │ ├── arr3d.rds │ ├── distil_result.rds │ ├── extract.gct.res.rds │ ├── matrices.rds │ ├── rnorm20.rds │ ├── rnorm_matrix.rds │ ├── robust_zs_rnorm20.rds │ ├── test_0.1_GCT.R │ ├── test_0.2_io.R │ ├── test_1_utils.R │ ├── test_3_math.R │ ├── test_GCT_class.R │ ├── test_cdesc.txt │ ├── test_deprecated.R │ ├── test_n5x10.gct │ └── test_n5x10.gctx └── vignettes └── tutorial.Rmd /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cmap/cmapR/HEAD/.dockerignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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