c3032bf7dcc4b8ecab30dcdee0b344d4 *DESCRIPTION
1ebbd3e34237af26da5dc08a4e440464 *LICENSE
be790c9837b6ea66eb2dbe8427d36dcd *NAMESPACE
793f4a0305d2c103867ebe0f8c47ccfb *R/TMB.R
ec7d3e1ec233208f54749f8d9a778b6a *R/getVarClass.R
0f32d978fd81f1494725b1c52450047d *R/getVarFeature.R
d2cecdb03e9e1df829157cc0230d451b *R/jointMAF.R
06d490e98517175655dfa0ae353247c9 *R/mutFilterAdj.R
f0a9e13f5fa8d57035e01d9700fac6ab *R/mutFilterCan.R
cd5130e51c0547c5af6ced55f28cd45a *R/mutFilterCom.R
1aa0659838670789d60b10c8963c3ccb *R/mutFilterDB.R
bb1e7911c508b9b388d7bc5952c1356f *R/mutFilterNormalDP.R
2e01759ff02cde4021140f3cc4a4e6ae *R/mutFilterPON.R
3df4b079c9bcfa4d5c9f2d8343964579 *R/mutFilterQual.R
a189d5f2352122d4eaf1f19155305e3a *R/mutFilterRef.R
f80607c368d956ebc2620383969103bd *R/mutFilterReg.R
1d31245d77a16f19d3d82fd9c0213c31 *R/mutFilterSB.R
5aca0c5af4af7b66063bee7dfeadefa6 *R/mutFilterTech.R
11dbc0d1fc81a6f8c2453f2e197b45a4 *R/mutFilterType.R
e1a038ce7e60aa91efb109aae0e1b924 *R/mutSelection.R
b95b4e284a39948610b82504a72f772f *R/processMut.R
2f12256e3be72319978402fa3cf8f2d7 *R/readBed.R
e0331826a869f8bb56cd4c5024b2b4cb *R/readINFO.R
5c9d3098c97c2b923817a3c19e9aab1c *R/selectMut.R
d9ac7a41b367fe4466d27b22eaadcf2f *R/selectTrans.R
ca80ea43acfe02daa874d83f6c66ea08 *R/toMesKit.R
5f4a2e23bd880c613beb28fc2045810f *R/tomaftools.R
5ce5dbd0602d189143c4ab0d80c2b75f *R/vcfToMAF.R
6bcd70e1be0511504b48712757ae3cb3 *README.md
63f1e7eefd9a13cf19dc1a00cb8773ef *build/vignette.rds
351b9a90b44f64bfa545b57e5842048d *inst/CITATION
f9992c6ddef0e53c1c701ae88edc3015 *inst/NEWS.md
52d3d707e01677c646098fe03b1aee2b *inst/doc/CaMutQC-manual.R
6574e47dd47f47d81b1b7ed00adc4ffc *inst/doc/CaMutQC-manual.Rmd
2683d478e85b50410435cfea57631b09 *inst/doc/CaMutQC-manual.html
2b97e6e5384eac0fa3720578ab047455 *inst/extdata/Multi-caller/WES_EA_T_1.MuSE.vep.vcf
c936a8a6dcbb3b4864e33a1ab680f3b6 *inst/extdata/Multi-caller/WES_EA_T_1_varscan_filter_snp.vep.vcf
05c161daeeb678baad2d9a40db1f7fe6 *inst/extdata/PON_test.txt
eb300e4c8d3248b498178a12b649d971 *inst/extdata/Panel_gene/FoundationOne_genelist.txt
60b10b65308b405a9843dbde6cf6a4a6 *inst/extdata/Panel_gene/MSK-IMPACT_gene_v1_341.txt
5bda3dd3491c42fa57fe051764bfc743 *inst/extdata/Panel_gene/MSK-IMPACT_gene_v2_410.txt
0baedbcaf32e14dfdbe37a2b9ec4d204 *inst/extdata/Panel_gene/MSK-IMPACT_gene_v3_468.txt
f3c2d225a88ffee30e5d046a6ace0537 *inst/extdata/Panel_gene/Pan-cancer_genelist.txt
4763020ae9fa5cc98fb85f1bf734c85a *inst/extdata/TSGenelist.txt
798751f5d19b42d4dc257c25cc94287c *inst/extdata/WES_EA_T_1_mutect2.vep.vcf
4a78b8891328edc07af1d359e8cbd6b8 *inst/extdata/bed/panel_hg19/FlCDx-hg19.rds
b1abb8040d7fc7a7c7717cbeae7c938f *inst/extdata/bed/panel_hg19/MSK_v1-hg19.rds
222c71146b1dd342505347c46181c71e *inst/extdata/bed/panel_hg19/MSK_v2-hg19.rds
5eea686f98ca76e6a510063065e7bd86 *inst/extdata/bed/panel_hg19/MSK_v3-hg19.rds
6c56b976d2b448a4f5b30efebb55c87c *inst/extdata/bed/panel_hg19/Pan-cancer-hg19.rds
82d6eafa94270328eaed66c6ae7433ca *inst/extdata/bed/panel_hg38/FlCDx-hg38.rds
de265ede6039b6fc7dec12d30d9e4576 *inst/extdata/bed/panel_hg38/MSK_v1-hg38.rds
fbd7eb863b878204d894840b422d0d7b *inst/extdata/bed/panel_hg38/MSK_v2-hg38.rds
4598c2e68e79bc2b75ab6d563d6b1db6 *inst/extdata/bed/panel_hg38/MSK_v3-hg38.rds
e937513586e80ac25c4004c4f6d2c96b *inst/extdata/bed/panel_hg38/Pan-cancer-hg38.rds
9f021b271be71d8f8929503b0e9a14f5 *inst/extdata/clin.txt
38b44d8d745e11e4eb03f7fb72256d11 *inst/extdata/noncoding.txt
6054c3efcb449301821c47aa4bbe58eb *inst/rmd/CaMutQC-FilterReport.Rmd
fae17326cad977848b0eab3dbbe8147a *inst/script/DATASETS
05c161daeeb678baad2d9a40db1f7fe6 *inst/shiny/dom/PON_example.txt
798751f5d19b42d4dc257c25cc94287c *inst/shiny/dom/example.vcf
a93a1cdae603f5fc53cf4fdaa45c4a99 *inst/shiny/server.R
edc471f96756bd892c058a43f90bf63a *inst/shiny/ui.R
642b496bf5ffbf98e5b3cf241f1df1ea *inst/shiny/www/CaMutQC_logo.png
36da7264a4f88041d0c9f472b207b46d *man/calTMB.Rd
0b61234eca49c51953a4c5dd8d93dc61 *man/mutFilterAdj.Rd
e66c3b7ea06beed7afe9232d7e6c7ed7 *man/mutFilterCan.Rd
3d6652abbf385355578d6281fde6a1ac *man/mutFilterCom.Rd
d6460aaf4f710671aa8beed6ac897ac9 *man/mutFilterDB.Rd
8eed3192f9e9ff75203149ec045bffc7 *man/mutFilterNormalDP.Rd
265bf067f8462203660a8e87f7276879 *man/mutFilterPON.Rd
7faaa73afc5229a488fe7076cada579c *man/mutFilterQual.Rd
f7d806dc66bff9e66e74d33534fa33de *man/mutFilterRef.Rd
0efc559be38179c17d24fb26893f0e90 *man/mutFilterReg.Rd
d8132c5b46b33e5415b5f8f354182bd3 *man/mutFilterSB.Rd
bbb42951d1df62c8fc67d1a23e9339aa *man/mutFilterTech.Rd
405d1ac0ea1320b545c55f53f196bf43 *man/mutFilterType.Rd
8dffa2eef46dba46653ce4ea5c862aa2 *man/mutSelection.Rd
e9480cb1a1f71ec47335d1204c31cc5b *man/processMut.Rd
d2c1368c7de1af99165a5cac6d57eb6e *man/toMesKit.Rd
b13f87332618f0df707aba5ee63055ab *man/tomaftools.Rd
784c5ed902f4a8517f6852971cfb267b *man/vcfToMAF.Rd
6574e47dd47f47d81b1b7ed00adc4ffc *vignettes/CaMutQC-manual.Rmd
89851186daf927bbc7ec5cc21de88fd9 *vignettes/CaMutQC-workflow.png
642b496bf5ffbf98e5b3cf241f1df1ea *vignettes/CaMutQC_logo.png
21b3c515aec45da189998ba9a4f9d56d *vignettes/Union_strategy.png
