Files in abemus
Adaptive Base Error Model in Ultra-Deep Sequencing Data
MD5
DESCRIPTION
README.md
NAMESPACE
inst/doc/abemus.html
inst/doc/abemus.Rmd
inst/extdata/regions_toy.bed
inst/extdata/test_sif_toy.tsv
inst/extdata/pacbam_data/TUMOR_A_toy.pabs
inst/extdata/pacbam_data/TUMOR_A_toy.pileup
inst/extdata/pacbam_data/CTRL_A_toy.pabs
inst/extdata/pacbam_data/CTRL_A_toy.pileup
inst/extdata/BaseErrorModel/afgtz.tsv
inst/extdata/BaseErrorModel/bperr_8.tsv
inst/extdata/BaseErrorModel/afz.RData
inst/extdata/BaseErrorModel/pbem_background.RData
inst/extdata/BaseErrorModel/bperr_summary.RData
inst/extdata/BaseErrorModel/afz_8.tsv
inst/extdata/BaseErrorModel/bperr.tsv
inst/extdata/BaseErrorModel/afz.tsv
inst/extdata/BaseErrorModel/afgtz_8.tsv
inst/extdata/BaseErrorModel/pbem_tab.RData
inst/extdata/Controls/minaf_cov_corrected_1r_0.995_b.RData
inst/extdata/Controls/tab1r_0.995_b.RData
inst/extdata/Controls/datathreshold.RData
inst/extdata/Results/filtering_criteria.txt
inst/extdata/Results/TUMOR_A_toy/pmtab_F2_TUMOR_A_toy.tsv
inst/extdata/Results/TUMOR_A_toy/pmtab_F3_TUMOR_A_toy.tsv
inst/extdata/Results/TUMOR_A_toy/pmtab_F1_TUMOR_A_toy.tsv
inst/extdata/Results/TUMOR_A_toy/pmtab_F3_optimalR_TUMOR_A_toy.tsv
inst/extdata/Results/TUMOR_A_toy/8/chrpm_f2.tsv
inst/extdata/Results/TUMOR_A_toy/8/chrpm_f1.tsv
inst/extdata/Results/TUMOR_A_toy/8/chrpm_f3.tsv
inst/extdata/pacbam_data_bychrom/TUMOR_A_toy/pileup/TUMOR_A_toy_chr8.pileup
inst/extdata/pacbam_data_bychrom/TUMOR_A_toy/snvs/TUMOR_A_toy_chr8.pabs
inst/extdata/pacbam_data_bychrom/CTRL_A_toy/pileup/CTRL_A_toy_chr8.pileup
inst/extdata/pacbam_data_bychrom/CTRL_A_toy/snvs/CTRL_A_toy_chr8.pabs
vignettes/abemus.Rmd
R/get_pbem.R
R/compute_afthreshold.R
R/get_case_mean_coverage.R
R/add_class_xbg.R
R/pos2bperr.R
R/split_pacbam_bychrom.R
R/get_tabcalls_path.R
R/strandbias.R
R/get_stats_pbem.R
R/bombanel_covs.R
R/apply_scaling_factor.R
R/CheckAltReads.R
R/add_class.R
R/fromListToDF.R
R/quantilezaf.R
R/filter.R
R/abemus.R
R/add_names.R
R/apply_AF_filters.R
R/bed2positions.R
R/import_sif.R
R/adjust_af_threshold_table.R
R/get_afth.R
R/compute_pbem.R
R/callsnvs.R
R/tab_optimal_R.R
R/get_germlineset.R
R/get_target_size.R
R/bombanel_afs.R
R/define_cov_bins.R
R/bombanel_tab_cov_pbem.R
R/compute_pbem_allele.R
man/callsnvs.Rd
man/compute_afthreshold.Rd
man/bed2positions.Rd
man/bombanel_tab_cov_pbem.Rd
man/get_target_size.Rd
man/bombanel_afs.Rd
man/abemus.Rd
man/get_case_mean_coverage.Rd
man/bombanel_covs.Rd
man/apply_scaling_factor.Rd
man/tab_optimal_R.Rd
man/compute_pbem.Rd
man/split_pacbam_bychrom.Rd
build/vignette.rds
data/bombanel_tab_cov_pbem.rda
data/tab_optimal_R.rda
data/bombanel_covs.rda
data/bombanel_afs.rda
data/datalist
