Files in MaximeWack/viroCapt
Viral capture analysis pipeline
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.org
R/functions.R
R/imports.R
R/pipeline.R
R/utils.R
R/visu.R
README.org
inst/hela/HELA_S21.R1.fastq.gz
inst/hela/HELA_S21.R2.fastq.gz
inst/hela/results/01_QC/HELA_S21.png
inst/hela/results/02_Global/HELA_S21.tsv
inst/hela/results/02_Global/HELA_S21.tsv.sel
inst/hela/results/03_Local/HELA_S21.png
inst/hela/results/03_Local/HELA_S21.sam
inst/hela/results/04_Fasta/HELA_S21.fa
inst/hela/results/05_Blat/HELA_S21.png
inst/hela/results/05_Blat/HELA_S21.tsv
inst/hela/results/05_Blat/HELA_S21_cleaned.tsv
inst/hela/results/05_Blat/HELA_S21_summary.tsv
inst/hela/results/06_Visu/HELA_S21.rds
inst/makefile
inst/refs/HPV1.fasta
inst/refs/HPV10.fasta
inst/refs/HPV101.fasta
inst/refs/HPV102.fasta
inst/refs/HPV103.fasta
inst/refs/HPV106.fasta
inst/refs/HPV107.fasta
inst/refs/HPV110.fasta
inst/refs/HPV111.fasta
inst/refs/HPV11_REF.fasta
inst/refs/HPV13.fasta
inst/refs/HPV16.fasta
inst/refs/HPV16_114-K.fasta
inst/refs/HPV16_16W12E.fasta
inst/refs/HPV16_AH2.fasta
inst/refs/HPV16_African-1.fasta
inst/refs/HPV16_African-1b.fasta
inst/refs/HPV16_Asian-American.fasta
inst/refs/HPV16_East-Asian.fasta
inst/refs/HPV16_European-German-131.fasta
inst/refs/HPV16_JP1773.fasta
inst/refs/HPV16_JPD169.fasta
inst/refs/HPV16_Qv15321AA.fasta
inst/refs/HPV16_Qv15351AA.fasta
inst/refs/HPV16_Qv15521E.fasta
inst/refs/HPV16_Qv16936E.fasta
inst/refs/HPV16_Qv17722E.fasta
inst/refs/HPV16_Qv18158E.fasta
inst/refs/HPV16_REF.fasta
inst/refs/HPV16_b.fasta
inst/refs/HPV16_c.fasta
inst/refs/HPV18.fasta
inst/refs/HPV18_BF380.fasta
inst/refs/HPV18_Qv02876.fasta
inst/refs/HPV18_Qv03132.fasta
inst/refs/HPV18_Qv03814.fasta
inst/refs/HPV18_Qv04924.fasta
inst/refs/HPV18_Qv15586.fasta
inst/refs/HPV18_Qv15957.fasta
inst/refs/HPV18_Qv16302.fasta
inst/refs/HPV18_Qv16306.fasta
inst/refs/HPV18_Qv17052.fasta
inst/refs/HPV18_Qv17199.fasta
inst/refs/HPV18_Qv17955.fasta
inst/refs/HPV18_Qv21444.fasta
inst/refs/HPV18_Qv21751.fasta
inst/refs/HPV18_Z135.fasta
inst/refs/HPV18_b.fasta
inst/refs/HPV1_a.fasta
inst/refs/HPV2.fasta
inst/refs/HPV20.fasta
inst/refs/HPV21.fasta
inst/refs/HPV22.fasta
inst/refs/HPV23.fasta
inst/refs/HPV24.fasta
inst/refs/HPV26.fasta
inst/refs/HPV27_b.fasta
inst/refs/HPV28.fasta
inst/refs/HPV29.fasta
inst/refs/HPV2_C1.fasta
inst/refs/HPV2_C2.fasta
inst/refs/HPV2_CN-HB1.fasta
inst/refs/HPV2_CN-SC1.fasta
inst/refs/HPV31_A.fasta
inst/refs/HPV31_REF.fasta
inst/refs/HPV32.fasta
inst/refs/HPV33.fasta
inst/refs/HPV33_REF.fasta
inst/refs/HPV34.fasta
inst/refs/HPV35_CG.fasta
inst/refs/HPV35_REF.fasta
inst/refs/HPV35_UA151.fasta
inst/refs/HPV35_UA3189.fasta
inst/refs/HPV35_UA3297.fasta
inst/refs/HPV36.fasta
inst/refs/HPV37.fasta
inst/refs/HPV38.fasta
inst/refs/HPV38_b-sub-FA125.fasta
inst/refs/HPV39_Qv36565.fasta
inst/refs/HPV39_REF.fasta
inst/refs/HPV4.fasta
inst/refs/HPV40_REF.fasta
inst/refs/HPV41.fasta
inst/refs/HPV42_REF.fasta
inst/refs/HPV42_TJ43-42.fasta
inst/refs/HPV43.fasta
inst/refs/HPV44.fasta
inst/refs/HPV45_BF134.fasta
inst/refs/HPV45_Qv00550.fasta
inst/refs/HPV45_Qv06560.fasta
inst/refs/HPV45_Qv20214.fasta
inst/refs/HPV45_Qv25000.fasta
inst/refs/HPV45_Qv26351.fasta
inst/refs/HPV45_Qv27565.fasta
inst/refs/HPV45_Qv30004.fasta
inst/refs/HPV45_Qv31035.fasta
inst/refs/HPV45_Qv31748.fasta
inst/refs/HPV45_Qv33330.fasta
inst/refs/HPV45_Qv34178.fasta
inst/refs/HPV45_Qv35960.fasta
inst/refs/HPV45_REF.fasta
inst/refs/HPV48.fasta
inst/refs/HPV49.fasta
inst/refs/HPV5.fasta
inst/refs/HPV50.fasta
inst/refs/HPV51_REF.fasta
inst/refs/HPV52_Qv15145.fasta
inst/refs/HPV52_REF.fasta
inst/refs/HPV53.fasta
inst/refs/HPV53_Qv04467.fasta
inst/refs/HPV53_Qv08183.fasta
inst/refs/HPV53_Qv17356.fasta
inst/refs/HPV53_Qv18622.fasta
inst/refs/HPV53_Qv20899.fasta
inst/refs/HPV53_Qv22707.fasta
inst/refs/HPV53_Qv23055.fasta
inst/refs/HPV53_Qv24231.fasta
inst/refs/HPV53_Qv30969.fasta
inst/refs/HPV53_Qv31688.fasta
inst/refs/HPV53_Qv32293.fasta
inst/refs/HPV53_Qv32783.fasta
inst/refs/HPV53_Qv33767.fasta
inst/refs/HPV54.fasta
inst/refs/HPV54_sub-AE9.fasta
inst/refs/HPV55.fasta
inst/refs/HPV56_Qv22608.fasta
inst/refs/HPV56_Qv24970.fasta
inst/refs/HPV56_Qv25665.fasta
inst/refs/HPV56_Qv26342.fasta
inst/refs/HPV56_Qv26458.fasta
inst/refs/HPV56_Qv26762.fasta
inst/refs/HPV56_REF.fasta
inst/refs/HPV57.fasta
inst/refs/HPV57_b.fasta
inst/refs/HPV57_c.fasta
inst/refs/HPV58_CNZJ-3.fasta
inst/refs/HPV58_JP1870.fasta
inst/refs/HPV58_REF.fasta
inst/refs/HPV58_sc100.fasta
inst/refs/HPV58_sc101.fasta
inst/refs/HPV58_sc144.fasta
inst/refs/HPV58_sc147.fasta
inst/refs/HPV58_sc165.fasta
inst/refs/HPV58_sc174.fasta
inst/refs/HPV58_sc185.fasta
inst/refs/HPV58_sc78.fasta
inst/refs/HPV59.fasta
inst/refs/HPV59_Qv33361.fasta
inst/refs/HPV5_b.fasta
inst/refs/HPV6.fasta
inst/refs/HPV60.fasta
inst/refs/HPV61.fasta
inst/refs/HPV62_Qv18091.fasta
inst/refs/HPV63.fasta
inst/refs/HPV65.fasta
inst/refs/HPV66.fasta
inst/refs/HPV66_Qv11088.fasta
inst/refs/HPV66_Qv218.fasta
inst/refs/HPV66_Qv24220.fasta
inst/refs/HPV66_Qv25111.fasta
inst/refs/HPV66_Qv25260.fasta
inst/refs/HPV66_Qv25662.fasta
inst/refs/HPV66_Qv25696.fasta
inst/refs/HPV66_Qv26488.fasta
inst/refs/HPV66_Qv26740.fasta
inst/refs/HPV66_Qv35854.fasta
inst/refs/HPV67.fasta
inst/refs/HPV67_Qv30703.fasta
inst/refs/HPV68_a.fasta
inst/refs/HPV69.fasta
inst/refs/HPV6_E.fasta
inst/refs/HPV6_LP238.fasta
inst/refs/HPV6_REF.fasta
inst/refs/HPV6_b.fasta
inst/refs/HPV7.fasta
inst/refs/HPV70.fasta
inst/refs/HPV71.fasta
inst/refs/HPV71_Qv21030.fasta
inst/refs/HPV71_Qv22792.fasta
inst/refs/HPV71_Qv22945.fasta
inst/refs/HPV71_Qv23143.fasta
inst/refs/HPV72_REF.fasta
inst/refs/HPV73_REF.fasta
inst/refs/HPV74_sub-AE10.fasta
inst/refs/HPV81.fasta
inst/refs/HPV82.fasta
inst/refs/HPV82_sub-IS39-AE2.fasta
inst/refs/HPV83.fasta
inst/refs/HPV84.fasta
inst/refs/HPV85_cand.fasta
inst/refs/HPV86_cand.fasta
inst/refs/HPV87_cand.fasta
inst/refs/HPV88.fasta
inst/refs/HPV89_cand.fasta
inst/refs/HPV8_CG.fasta
inst/refs/HPV9.fasta
inst/refs/HPV90.fasta
inst/refs/HPV91.fasta
inst/refs/HPV92.fasta
inst/refs/HPV93.fasta
inst/refs/HPV94.fasta
inst/refs/HPV94_nearly-Korean-variant.fasta
inst/refs/HPV96.fasta
inst/refs/HPV97.fasta
inst/refs/HPV97_624.fasta
inst/refs/HPV97_W15189.fasta
inst/refs/HPVFA75_KI88-03.fasta
inst/refs/HPVRTRX7.fasta
inst/refs/HPVs.fasta
inst/refs/ctrl_capture.fasta
inst/visu/server.R
inst/visu/ui.R
