Files in msk-access/access_data_analysis

ACCESS data analysis

.Rbuildignore

.gitbook.yaml

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/CNA_processing.R R/SV_incorporation.R R/cna_divide_by_sample.R R/compile_reads.R R/compile_reads_all.R R/filter_calls.R R/plot_all_events.R

README.html

README.md SUMMARY.md

data/._example_master_file.csv

data/._example_master_file_raw.csv

data/example_master_file.csv

data/example_master_file_raw.csv

docs/README.md docs/SUMMARY.md docs/analysis/cna-processing.md docs/analysis/compile-reads.md docs/analysis/create-report.md docs/analysis/filter-calls.md docs/analysis/intermediate-file-organization.md docs/analysis/overview-of-analysis-workflow.md docs/analysis/sv-incorporation.md docs/setup/cna-result-processing.md docs/setup/installation.md docs/setup/resources.md docs/setup/setup-for-running-analysis.md

juno_setup/._softlinking_bams.sh

juno_setup/README.md juno_setup/process_master_file.R

juno_setup/softlinking_bams.sh

python/convert_csv_to_maf/README.md

python/convert_csv_to_maf/csv_to_maf.py

python/convert_csv_to_maf/example_output.maf.txt

python/convert_csv_to_maf/example_output.xlsx

python/convert_csv_to_maf/fof.txt

python/convert_csv_to_maf/requirements.txt

python/convert_dates_to_days/README.md

python/convert_dates_to_days/convert_dates_to_days.py

python/convert_dates_to_days/example_input.txt

python/convert_dates_to_days/output.txt

python/get_cbioportal_variants/README.md

python/get_cbioportal_variants/example_output.maf

python/get_cbioportal_variants/get_cbioportal_variants.py

python/get_cbioportal_variants/requirements.txt

python/run_create_report/README.md

python/run_create_report/modules/check_required_columns.py

python/run_create_report/modules/generate_create_report_cmd.py

python/run_create_report/modules/generate_facet_maf_path.py

python/run_create_report/modules/generate_repo_paths.py

python/run_create_report/modules/get_small_variant_csv.py

python/run_create_report/modules/read_manifest.py

python/run_create_report/modules/run_cmd.py

python/run_create_report/requirement.txt

python/run_create_report/run_create_report.py

reports/create_report.R

reports/style.css

reports/template.Rmd reports/template_days.Rmd

msk-access/access_data_analysis documentation built on Nov. 13, 2023, 12:43 p.m.