Files in alex-kalinka-cruk/fgcQC
QC metric calculations for CRISPR screen data produced at the FGC
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/GICC.R
R/NNMD.R
R/NNMD_robust.R
R/QC_fgc_crispr_data.R
R/add_ROC.R
R/add_ROC_gene_sets.R
R/add_bagel_PRROC_gene_sets.R
R/assemble_counts_QC.R
R/assemble_logfc_QC.R
R/bagel.fgc_0008.R
R/calc_AUC.R
R/calc_GC_percent_library.R
R/calc_GICC_gene_sets.R
R/calc_NNMD_gene_sets.R
R/calc_NNMD_robust_gene_sets.R
R/calc_dcorr_GC_content_counts.R
R/calc_dcorr_GC_content_logfc.R
R/calc_dispersion_adj_gRNA.R
R/calc_gini_coefficient_counts.R
R/calc_inefficient_gRNA_count_ratios.R
R/calc_inefficient_gRNA_logfc.R
R/calc_log2_fold_change_gRNAs.R
R/calc_log2_fold_change_genes.R
R/calc_low_zero_count_plasmid_gRNAs.R
R/calc_mahalanobis_dist_plasmid.R
R/calc_percent_matching_gRNAs.R
R/calc_replicate_logfc_corr.R
R/cleanr.lfc.fgc_0008.R
R/config_qc_metrics.R
R/counts.fgc_0008.R
R/crispr_gene_sets.R
R/extract_analysis_comparisons.R
R/extract_b2f_json.R
R/extract_proximal_4bases_PAM.R
R/fgcQC-package.R
R/get_PRROC.R
R/mask_mocked_columns.R
R/merge_bcl2fastq_config_qc.R
R/mock_bcl2fastq_json.R
R/mock_bcl2fastq_template.R
R/mock_config_qc_section.R
R/mock_library_cleanr_tsv.R
R/mock_missing_FGC_data.R
R/normalize_library_depth_median_ratio.R
R/normalize_library_depth_relative.R
R/print.fgcQC.R
R/read_analysis_config_json.R
R/summarise_samples_bcl2fastq.R
README.md
data/bagel.fgc_0008.rda
data/cleanr.lfc.fgc_0008.rda
data/config_qc_metrics.rda
data/counts.fgc_0008.rda
data/crispr_gene_sets.rda
data/mask_mocked_columns.rda
data/mock_bcl2fastq_template.rda
fgcQC.Rproj
man/GICC.Rd
man/NNMD.Rd
man/NNMD_robust.Rd
man/QC_fgc_crispr_data.Rd
man/add_ROC.Rd
man/add_bagel_PRROC_gene_sets.Rd
man/add_bagel_ROC_gene_sets.Rd
man/assemble_counts_QC.Rd
man/assemble_logfc_QC.Rd
man/bagel.fgc_0008.Rd
man/calc_AUC.Rd
man/calc_GC_percent_library.Rd
man/calc_GICC_gene_sets.Rd
man/calc_NNMD_gene_sets.Rd
man/calc_NNMD_robust_gene_sets.Rd
man/calc_dcorr_GC_content_counts.Rd
man/calc_dcorr_GC_content_logfc.Rd
man/calc_dispersion_adj_gRNA.Rd
man/calc_gini_coefficient_counts.Rd
man/calc_inefficient_gRNA_count_ratios.Rd
man/calc_inefficient_gRNA_logfc.Rd
man/calc_log2_fold_change_gRNAs.Rd
man/calc_log2_fold_change_genes.Rd
man/calc_low_zero_count_plasmid_gRNAs.Rd
man/calc_mahalanobis_dist_plasmid.Rd
man/calc_median_normalization_size_factors.Rd
man/calc_percent_matching_gRNAs.Rd
man/calc_replicate_logfc_corr.Rd
man/cleanr.lfc.fgc_0008.Rd
man/config_qc_metrics.Rd
man/counts.fgc_0008.Rd
man/crispr_gene_sets.Rd
man/extract_analysis_comparisons.Rd
man/extract_b2f_json.Rd
man/extract_proximal_4bases_PAM.Rd
man/fgcQC-package.Rd
man/get_PRROC.Rd
man/mask_mocked_columns.Rd
man/merge_bcl2fastq_config_qc.Rd
man/mock_bcl2fastq_json.Rd
man/mock_bcl2fastq_template.Rd
man/mock_config_qc_section.Rd
man/mock_library_cleanr_tsv.Rd
man/mock_missing_FGC_data.Rd
man/normalize_library_depth_median_ratio.Rd
man/normalize_library_depth_relative.Rd
man/print.fgcQC.Rd
man/read_analysis_config_json.Rd
man/summarise_samples_bcl2fastq.Rd
tests/testthat.R
tests/testthat/test-bagel.R
tests/testthat/test-counts.R
tests/testthat/test-gicc.R
tests/testthat/test-logfc.R
vignettes/.gitignore
vignettes/summary.Rmd
