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‎.Rbuildignore

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^vignettes/.*gml$
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^.*\.Rproj$
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^\.Rproj\.user$
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^inst/shinyapp/Rambow_dataset/.*$
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^inst/shinyapp/Small_dataset/.*$
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^inst/shinyapp/Rambow_dataset$
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^inst/shinyapp/Small_dataset$

‎.gitignore

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/vignettes/lg_output.xml
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/doc/
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/Meta/
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/inst/shinyapp/Rambow_dataset
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/inst/shinyapp/Rambow_dataset/*
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/inst/shinyapp/Small_dataset
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/inst/shinyapp/Small_dataset/*

‎R/zzz.R

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‎inst/shinyapp/Rambow_dataset/config/.config_01_m.yml

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sc_metadata_file:
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files:
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'0':
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- ''
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- Rambow_dataset
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- data_info.rds
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root: ..
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m_time_column: Age
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m_time_points:
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- before treatment
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- 4d on treatment
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- 28d on treatment
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- 57d on treatment
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m_id_column: Run

‎inst/shinyapp/Rambow_dataset/config/.config_02_av.yml

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av_vcf_out_dir:
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path:
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- ''
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- Rambow_dataset
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- vcf_out
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root: ..
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av_anovar_exec_dir:
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path:
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- ''
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- Rambow_dataset
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- annovar
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root: ..
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av_anovar_db_dir:
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path:
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- ''
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- Rambow_dataset
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- annovar
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- RefGene_hg38
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root: ..
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av_vcf_in_dir:
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path:
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- ''
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- Rambow_dataset
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- vcf
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root: ..

‎inst/shinyapp/Rambow_dataset/config/.config_03_thr.yml

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thr_vcf_in_dir:
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path:
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- ''
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- Rambow_dataset
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- vcf_out
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root: ..
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thr_out_dir:
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path:
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- ''
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- Rambow_dataset
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- filtered_vcf
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root: ..
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thr_alleles_ratio: 2
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thr_maf: 0.01
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thr_freq: 0.05
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thr_accepted_var:
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- stopgain
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- stoploss
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- nonframeshift insertion
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- nonframeshift block substitution
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- nonsynonymous SNV
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- frameshift block substitution
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- frameshift insertion
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- frameshift deletion
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- nonframeshift deletion
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thr_negleted_var:
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- synonymous SNV
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- unknown
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‎inst/shinyapp/Rambow_dataset/config/.config_04_dp.yml

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dp_out_dir:
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path:
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- ''
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- Rambow_dataset
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- sam_out
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root: ..
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dp_samtools_exec_dir:
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path:
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- ''
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- usr
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- bin
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root: Computer
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dp_bam_dir:
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path:
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- ''
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- Rambow_dataset
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- bam
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root: ..
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dp_mut_dir:
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path:
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- ''
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- Rambow_dataset
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- filtered_vcf
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root: ..

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