Package index • dracarys

All functions

BcftoolsStatsFile: BcftoolsStatsFile R6 Class

BclconvertReports: BclconvertReports R6 Class

BclconvertReports375: BclconvertReports375 R6 Class

FastqcMetricsFile: FastqcMetrics R6 Class

File: File R6 Class

FragmentLengthHistFile: FragmentLengthHistFile R6 Class

MappingMetricsFile: MappingMetricsFile R6 Class

MultiqcFile: MultiqcFile R6 Class

PcgrJsonFile: PcgrJson R6 Class

PcgrTiersFile: PcgrTiersFile R6 Class

PloidyEstimationMetricsFile: PloidyEstimationMetricsFile R6 Class

ReplayFile: ReplayFile R6 Class

SvMetricsFile: SvMetricsFile R6 Class

TimeMetricsFile: TimeMetricsFile R6 Class

TrimmerMetricsFile: TrimmerMetricsFile R6 Class

VCMetricsFile: VCMetricsFile R6 Class

Wf: Workflow

Wf_sash: Wf_sash R6 Class

Wf_sash_download_tidy_write(): sash Download Tidy and Write

Wf_tso_ctdna_tumor_only: Wf_tso_ctdna_tumor_only R6 Class

Wf_tso_ctdna_tumor_only_v2: Wf_tso_ctdna_tumor_only_v2 R6 Class

Wf_umccrise: Wf_umccrise R6 Class

Wf_umccrise_download_tidy_write(): umccrise Download Tidy and Write

WgsContigMeanCovFile: WgsContigMeanCovFile R6 Class

WgsCoverageMetricsFile: WgsCoverageMetricsFile R6 Class

WgsFineHistFile: WgsFineHistFile R6 Class

WgsHistFile: WgsHistFile R6 Class

bcftools_parse_vcf(): Parse VCF with bcftools

bcftools_parse_vcf_regions(): Parse VCF regions with bcftools

date_log(): Print current timestamp for logging

dr_func_eval(): Evaluate dracarys Function

dr_gds_download(): dracarys GDS Download

dr_output_format_valid(): Output Format is Valid

dr_s3_download(): dracarys S3 Download

dtw_Wf_tso_ctdna_tumor_only(): Wf_tso_ctdna_tumor_only Download Tidy and Write

dtw_Wf_tso_ctdna_tumor_only_v2(): Wf_tso_ctdna_tumor_only_v2 Download Tidy and Write

empty_tbl(): Create Empty Tibble Given Column Names

file_regex_getter(): Get dracarys DR_FILE_REGEX

gds_file_download_api(): GDS File Download via API

gds_file_download_cli(): GDS File Download via CLI

gds_file_presignedurl(): GDS File Presigned URL

gds_files_list_fastq(): List FASTQs In GDS Directory

gds_list_files_dir(): List Files in ICAv1 GDS Directory

gds_list_files_filter_relevant(): List Relevant Files In ICAv1 GDS Directory

gds_volumes_list(): List GDS Volumes

grep_file(): Grep File Pattern

ica_token_validate(): Validate ICA access token

local_list_files_dir(): List Files in Local Directory

local_list_files_filter_relevant(): List Relevant Files In Local Directory

match_regex(): Match File to Regex

multiqc_column_map_append(): Append New MultiQC Workflow Columns

multiqc_date_fmt(): Format MultiQC Config Date

multiqc_parse_bargraph_plot(): MultiQC Extract Bar Graph Data

multiqc_parse_gen(): Parse MultiQC 'report_general_stats_data' JSON Element

multiqc_parse_plots(): Parse Plot Data from MultiQC JSON

multiqc_parse_raw(): Parse MultiQC 'report_saved_raw_data' JSON Element

multiqc_parse_raw_interop(): Parse Interop MultiQC 'report_saved_raw_data' JSON Element

multiqc_parse_xyline_plot(): MultiQC Extract XY Line Plot Data

multiqc_parse_xyline_plot_contig_cvg(): MultiQC Extract XY Line Plot Data for DRAGEN Contig Coverage

multiqc_tidy_json(): Tidy MultiQC JSON

rdf2tab(): Write Local R Dataframe to Spark-backed Table

read(<File>): Read File object

read(): Generic Reading

s3_file_presignedurl(): S3 Generate Presigned URL

s3_list_files_dir(): List Objects in AWS S3 Directory

s3_list_files_filter_relevant(): List Relevant Files In AWS S3 Directory

s3_search(): Search AWS S3 Objects

session_info_kable(): Session Information Kable

tidy_files(): Tidy Files

time_metrics_process(): Process Multiple TimeMetricsFile Objects

tso_acfc_plot(): Plot ACFC

tso_acfc_read(): Read TSO AlignCollapseFusionCaller_metrics File

tso_combinedvaro_smallv_read(): Read TSO CombinedVariantOutput File

tso_fraglenhist_plot(): Plot Fragment Length Hist

tso_fusions_read(): Read TSO Fusions File

tso_msi_read(): Read TSO MSI JSON File

tso_sar_read(): Read TSO SampleAnalysisResults JSON File

tso_targetregcvg_plot(): Plot TargetRegionCoverage

tso_targetregcvg_read(): Read TSO TargetRegionCoverage File

tso_tmbt_read(): Read TSO TMB_Trace File

umccr_tidy(): Tidy UMCCR Results

write_dracarys_list_of_tbls(): Write List of Tidy Tibbles