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 |
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