Files in cgrlab/TypeSeqHPV

TypeSeqHPV Analysis Functions and Workflows

.gitignore

DESCRIPTION

NAMESPACE

R/calculate_expected_control_results.R R/coinfection_rate_histogram.R R/convert_bam_to_json.R R/create_full_run_read_metrics_df.R R/create_hpv_types_table.R R/create_inital_pos_neg_matrix.R R/finalize_pn_matrix.R R/get_run_metadata.R R/hpv_status_circle_plot.R R/ion_read_processor.R R/lineage_plot.R R/percent_positve_histogram.R R/plate_summary.R R/prepare_grouped_samples_only_matrix_outputs.R R/prepare_lineage_df.R R/read_in_bam_header.R R/read_in_parameters_csv.R R/render_report.R R/sample_summary.R R/samtools_extract_header.R R/scaling_of_b2m_human_control.R R/signal_to_noise_plot.R R/split_pn_matrix_into_multiple_deliverables.R R/startplugin_parse.R R/ts_demultiplex_bc2.R R/ts_read_metrics.R R/write_all_csv_files.R README.md

docker/Dockerfile.dev

docker/Dockerfile.prd

docker/base_Dockerfile

docs/CONTROLS_TypeSeq_Control_Definitions.csv

docs/GROUPINGS_TypeSeq_Definitions.csv

docs/Ion/2017-06-11_Pos-Neg_matrix_filtering_criteria_RefTable_v3.txt

docs/Ion/2017-11-24_TypeSeqer_Filtering_Scaling_Table_v2.csv

docs/Ion/20180121_lineage_reference_table_and_filters_2.csv

docs/Ion/TypeSeqer_Ion_Custom_Barcode_Series.csv

docs/Ion/TypeSeqer_Ion_Custom_Reference.fasta

docs/Ion/TypeSeqer_Ion_Dual-Barcodes_For-Manifest-Preparation.xlsx

docs/Ion/barcodeList_TypingV1_v2-barcodes.csv

docs/Ion/barcodeList_v1.txt

docs/Ion/hpv_types_MQ_min_max_len_filters_JUNE2017_30-10bpLen_v6.txt

docs/SAMPLE_MANIFEST_TypeSeq_ILLUMINA-EXAMPLE.csv

docs/SAMPLE_MANIFEST_TypeSeq_ION-EXAMPLE.csv

docs/SAMPLE_MANIFEST_TypeSeq_Template.csv

docs/TypeSeq_HPV_Analysis_Instructions.pdf

docs/example_results/CONTROLS_TypeSeq_Control_Definitions.csv

docs/example_results/Example-B1_control_results.csv

docs/example_results/Example-B1_failed_samples_matrix.csv

docs/example_results/Example-B1_full_pn_matrix.csv

docs/example_results/Example-B1_hpv_read_counts_matrix.csv

docs/example_results/Example-B1_lineage_matrix.csv

docs/example_results/Example-B1_qc_report.pdf

docs/example_results/Example-Project1_Example-B1_samples_only_matrix.csv

docs/example_results/Example-Project2_Example-B1_samples_only_matrix.csv

docs/example_results/Example-Project3_Example-B1_samples_only_matrix.csv

docs/example_results/GROUPINGS_TypeSeq_Custom_Grouping_Definitions.csv

docs/example_results/SAMPLE_MANIFEST_Example-for-github.csv

inst/ion_plugin_specific_files/create_plugin_zip.sh

inst/ion_plugin_specific_files/instance.html

inst/ion_plugin_specific_files/launch.sh

inst/ion_plugin_specific_files/plan.html

inst/ion_plugin_specific_files/pluginsettings.json

inst/reports/Ion_Torrent_report.R inst/reports/torrent_server_html_block.R workflows/ion_workflow.R

cgrlab/TypeSeqHPV documentation built on Jan. 11, 2023, 9:21 p.m.