Man pages for cancerdatasci/ceres
CERES for R
| align.dataset.margins | align dataset margins |
| cluster_cn | Hierarchically cluster copy number data |
| collapse_rows_of_matrix | convert matrix to data frame |
| collate_ceres_results | Collate CERES results |
| df.to.mat | convert data frame to matrix |
| evaluate_prediction_auc | Calculate area under the curve for ROC and PR curves. |
| fetchPAM | Get a PAM sequence |
| generate_guides | Generation of the guides from a gct dep_file |
| guideAlignments | Read BAM file report, filter with valid PAM sequence, report... |
| intersect_data_with_segment | Finds overlaps between target segments and data. Calculates... |
| intersect_gene_with_copy_number | Get a matrix of CN for genes |
| intersect_guide_with_copy_number | Get a matrix of CN for CRISPR target sites |
| intersect_locus_with_cn_seg | Intersect locus with copy number segment |
| make.a.tidy.dataset | make a tidy dataset |
| map_guide_to_locus | Map guide to locus |
| mat.to.df | convert matrix to data frame |
| prepare_ceres_inputs | CERES main routine |
| read.gct | read a *.gct file into your session |
| read.gmt | read a *.gmt file into your session |
| remove.cols.all.nas | remove columns from a matrix that include any NAs |
| remove.cols.any.nas | remove columns from a matrix that are entirely NAs |
| remove.rows.all.nas | remove rows from a matrix that include any NAs |
| remove.rows.any.nas | remove rows from a matrix that are entirely NAs |
| run_ceres | CERES main routine |
| run_precision_recall | Run precision recall assessment using essential and... |
| scale_to_essentials | Normalize CERES gene effects according to essential and... |
| wrap_ceres | CERES wrapper |
| write.gct | write a *.gct file to disk |
