├── .gitignore ├── DESCRIPTION ├── LICENSE.txt ├── NAMESPACE ├── R ├── RcppExports.R ├── cluster_cn.R ├── cn_seg_intersect.R ├── collate_ceres_results.R ├── dataset_utils.R ├── evaluate_prediction_auc.R ├── fileIO.R ├── guide_alignments.R ├── prepare_inputs.R ├── run_ceres.R ├── run_precision_recall.R ├── scale_to_essentials.R └── wrap_ceres.R ├── README.md ├── ceres.Rproj ├── data ├── hart_essentials.RData └── hart_nonessentials.RData ├── man ├── align.dataset.margins.Rd ├── cluster_cn.Rd ├── collapse_rows_of_matrix.Rd ├── collate_ceres_results.Rd ├── df.to.mat.Rd ├── evaluate_prediction_auc.Rd ├── fetchPAM.Rd ├── generate_guides.Rd ├── guideAlignments.Rd ├── intersect_data_with_segment.Rd ├── intersect_gene_with_copy_number.Rd ├── intersect_guide_with_copy_number.Rd ├── intersect_locus_with_cn_seg.Rd ├── make.a.tidy.dataset.Rd ├── map_guide_to_locus.Rd ├── mat.to.df.Rd ├── prepare_ceres_inputs.Rd ├── read.gct.Rd ├── read.gmt.Rd ├── remove.cols.all.nas.Rd ├── remove.cols.any.nas.Rd ├── remove.rows.all.nas.Rd ├── remove.rows.any.nas.Rd ├── run_ceres.Rd ├── run_precision_recall.Rd ├── scale_to_essentials.Rd ├── wrap_ceres.Rd └── write.gct.Rd └── src ├── .gitignore ├── RcppExports.cpp └── ceresv51.cpp /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cancerdatasci/ceres/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cancerdatasci/ceres/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cancerdatasci/ceres/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /NAMESPACE: 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