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 |

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 |

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