Files in bahlolab/exSTRa

Expanded STR algorithm: detecting expansions in Illumina sequencing data

.Rbuildignore

.github/.gitignore

.github/workflows/check_standard.yml

.github/workflows/r.yml

.github/workflows/test-coverage.yaml

.gitignore

.travis.yml

DESCRIPTION

LICENCE

NAMESPACE

R/CLASS_exstra_db.R R/CLASS_exstra_score.R R/CLASS_exstra_tsum.R R/GENERICS.R R/add_alpha_.R R/exstra_known.R R/exstra_wgs_pcr_2.R R/filter_low_scores.R R/filter_sex.R R/ggplot.exstra_score.R R/loci_normal_expansion.R R/p_values.R R/plot_multi.R R/private_functions.R R/rbind_score_list.R R/read_exstra_db.R R/read_exstra_db_known.R R/read_exstra_db_txt_guesser.R R/read_exstra_db_ucsc.R R/read_exstra_db_xlsx.R R/read_score.R R/suggested_exstra_pipeline.R R/tsum_p_value_summary.R R/tsum_test.R R/zzz.R README.md

codecov.yml

data-raw/exstra_known.R data-raw/exstra_wgs_pcr_2.R

data/exstra_known.RData

data/exstra_wgs_pcr_2.RData

doc/exSTRa.R doc/exSTRa.Rmd

doc/exSTRa.html

doc/simpleRepeats.R doc/simpleRepeats.Rmd

doc/simpleRepeats.html

exSTRa.Rproj

examples/.gitignore

examples/exSTRa_score_analysis.R examples/exSTRa_suggested_pipeline.pdf

inst/CITATION

inst/TODO.md

inst/extdata/HiSeqXTen_WGS_PCR_2.txt

inst/extdata/exSTRa_pipeline_graph.gv

inst/extdata/repeat_expansion_disorders_grch37.txt

inst/extdata/repeat_expansion_disorders_grch38.txt

inst/extdata/repeat_expansion_disorders_hg19.txt

inst/extdata/repeat_expansion_disorders_hg38.txt

inst/tools/giab_read_extraction.R inst/tools/prepare_exSTRa_input_db.R man/add_alpha_.Rd man/as.exstra_score.Rd man/copy.Rd man/exSTRa.Rd man/exstra_known.Rd man/exstra_score_new_.Rd man/exstra_tsum_new_.Rd man/exstra_wgs_pcr_2.Rd man/filter_low_scores.Rd man/filter_sex.Rd man/ggexstra_ecdf.Rd man/ggplot.exstra_score.Rd man/is.exstra_db.Rd man/is.exstra_score.Rd man/is.exstra_tsum.Rd man/loci.Rd man/loci_min_exp.Rd man/loci_normal.Rd man/loci_normal_exp.Rd man/loci_text_info.Rd man/p_value_sd_.Rd man/p_values.Rd man/plot.exstra_score.Rd man/plot.exstra_tsum.Rd man/plot_multi.Rd man/plot_names-set.Rd man/plot_names.Rd man/qm_tsum_stat_bare_.Rd man/rbind_score_list.Rd man/read_exstra_db.Rd man/read_exstra_db_ucsc.Rd man/read_score.Rd man/sub-.exstra_score.Rd man/sub-.exstra_tsum.Rd man/suggested_exstra_pipeline.Rd man/tsum_p_value_summary.Rd man/tsum_test.Rd tests/testthat.R tests/testthat/setup_tsum_object.R tests/testthat/test-CLASS_exstra_db.R tests/testthat/test-add_alpha_.R tests/testthat/test-exstra_score.R tests/testthat/test-exstra_tsum.R tests/testthat/test-p_values.R tests/testthat/test-plot_multi.R tests/testthat/test-read_score.R tests/testthat/test-suggested_exstra_pipeline.R tests/testthat/test_number_names.R tests/testthat/test_rbind_score_list.R tests/testthat/test_tsum_statistic_on_qm.R tests/testthat/test_tsum_test.R tests/testthat/test_with_large_data.R vignettes/exSTRa.Rmd

vignettes/images/ucsc_table_browser.png

vignettes/simpleRepeats.Rmd

bahlolab/exSTRa documentation built on Sept. 17, 2022, 5:08 p.m.