Files in cgrlab/TypeSeqHPV
TypeSeqHPV Analysis Functions and Workflows

.gitignore
DESCRIPTION
NAMESPACE
R/adam_demux.R R/calculate_expected_control_results.R R/coinfection_rate_histogram.R R/control_summary.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/illumina_read_processor_load_packages.R R/install_binaries.R R/ion_read_processor.R R/ion_read_processor_load_packages.R R/ion_report_get_args.R R/ion_report_load_packages.R R/lineage_plot.R R/methyl_command_line_args.R R/methyl_startplugin_parse.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/samtools_sort.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/tvc_run.R R/vcf_2_dataframe.R R/write_all_csv_files.R README.md
TypeSeqHPVMethyl_Plugin_Dev.zip
docker/ADAM_Dockerfile
docker/Dockerfile
docker/base_docker/Dockerfile
docs/CONTROLS_TypeSeq_Control_Definitions.csv
docs/GROUPINGS_TypeSeq_Definitions.csv
docs/Illumina/2017-06-11_Pos-Neg_matrix_filtering_criteria_RefTable_v3.txt
docs/Illumina/2017-11-24_TypeSeqer_Filtering_Scaling_Table_v2.csv
docs/Illumina/TypeSeqer_Illumina_Barcode_List.csv
docs/Illumina/TypeSeqer_Illumina_Dual-Barcodes_For-Manifest-Preparation.xlsx
docs/Illumina/illumina_TypeSeqer_minQual_minLen_filters.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/methylation/barcodes.csv
inst/methylation/create_plugin_zip.sh
inst/methylation/demux_3prime_barcode_adam.scala
inst/methylation/instance.html
inst/methylation/launch.sh
inst/methylation/plan.html
inst/methylation/pluginsettings.json
inst/methylation/torrent_server_html_block.R
inst/methylation/vcf_to_json_adam.scala
inst/reports/Ion_Torrent_report.R inst/reports/torrent_server_html_block.R inst/sig2noise/signal_to_noise.R workflows/dag.R workflows/illumina_read_processor.R workflows/ion_methyl_workflow.R workflows/ion_workflow.R
cgrlab/TypeSeqHPV documentation built on March 24, 2019, 10:13 a.m.