291478599529d850b68b9f4c93984c33 *DESCRIPTION
8266d81f797b7c152fca7d2d0b62780f *NAMESPACE
bf57917e041c9a85036aa15108eeb7f2 *NEWS
f63c5de348d4e1a98a21d543e1d72ca4 *R/BaalChIP-checks.R
fb3c9e4f6cf196015fc56f420c1e8ba5 *R/BaalChIP-class.R
de2e66e32e477c6efaab8aa1aa8a0ba3 *R/BaalChIP-generics.R
d5c380d5fb47702ae5b15a5b472bc621 *R/BaalChIP-methods.R
212e95c8283e8224bffef5f5f45523ab *R/Bayes_report.R
e56e512049a273e99ce13e52936ec364 *R/QCIntBias.R
28142bd848f564853029c54be6ef7732 *R/QCmerged.R
ec598480dd309af2e0f98085c108b215 *R/QCperBam.R
a57a37a96b99cb07acd464d3ee460461 *R/allASBbias.R
7250ea0b326fea4b742b8d2aade540d5 *R/alleleCounts.R
481b558ece35f98f86d9df6ffafa7379 *R/allplots.R
e7859c830f5306d0b5ef21e09f629a00 *R/allsummary.R
8229321c52318e7869ec593c253fe4ad *R/applyBayes.R
c7ebe162d6641fc020ca165ba645dbce *README.md
a06661c6e171d1315bf9fadd5deadf67 *build/vignette.rds
d95517f61e8b5c13ac3b690b6d4a5374 *data/ENCODEexample.RData
ff2cf54215f48bd0a0f31a17260ae77e *data/FAIREexample.RData
ce7119168782aa4d3d956e5141ed2550 *data/UniqueMappability50bp_hg19.RData
23157446333dd01c1d006e3ec001c153 *data/baalObject.RData
0fc3e759a27e99aca01e87633cc9287b *data/blacklist_hg19.RData
238836dcba18728bd32c69aa762eca44 *data/datalist
76fae85b0476bd5fed6d28ac130410cd *data/pickrell2011cov1_hg19.RData
12b612d8f44403bbeb5131c86834548b *inst/CITATION
4bcb45dbd3b162add13ad8b58754af8c *inst/doc/BaalChIP.R
d150e9563a6eaff6465ff1abb9fa974c *inst/doc/BaalChIP.Rmd
8efb5dae5cc4e3ebfa23735bfe0759f8 *inst/doc/BaalChIP.html
f3740b5b23040b009ef3773971635469 *inst/extra/get.overlaps.v2_chrXY.perl
2839f9d957e8408f360a73c807dc577d *inst/extra/run_simulations.sh
aef76ff89c48aba2836b3513c48f19f7 *inst/test/AMOVC_hetSNP.txt
6f96297112143141b7722d1d8e1fd20d *inst/test/GM12891_hetSNP.txt
14febf61389ef198586e9074ba9eaca8 *inst/test/MCF7_hetSNP.txt
c1be60bd8936a53b079829368f57d76c *inst/test/TaT1_hetSNP.txt
49acfc2455f48ad0190affee3372a634 *inst/test/bamFiles/AMOVC_1.test.bam
1c1cc28d69259e2c87422d61205f539b *inst/test/bamFiles/AMOVC_1.test.bam.bai
f67f8ecb8ea2d66c30a1122a826a6af8 *inst/test/bamFiles/AMOVC_1_gDNA.test.bam
d18eba452a93662a289675442e94f1f5 *inst/test/bamFiles/AMOVC_1_gDNA.test.bam.bai
6d5bf9cfd0dedeedef41bfd5443fb5d6 *inst/test/bamFiles/AMOVC_2.test.bam
be60f1e7b165c1c1d0652e9ffd679c9e *inst/test/bamFiles/AMOVC_2.test.bam.bai
b3ce873d07f0e6ae99abb9d9b6ecfe3c *inst/test/bamFiles/AMOVC_2_gDNA.test.bam
128b4d27f35763fc65bc44cbc45ac902 *inst/test/bamFiles/AMOVC_2_gDNA.test.bam.bai
028c88d8fb7fef3f0442989943a78e51 *inst/test/bamFiles/GM12891_PAX5_Rep1.bam
17324b40c7882848277978bedc306465 *inst/test/bamFiles/GM12891_PAX5_Rep1.bam.bai
f5e867bdc8995501db93f171735c3f68 *inst/test/bamFiles/GM12891_PAX5_Rep2.bam
0ff0682341c9144b5daee17c44edcb47 *inst/test/bamFiles/GM12891_PAX5_Rep2.bam.bai
91983547913597ab2053ab19fe64a248 *inst/test/bamFiles/GM12891_POL2_Rep1.bam
61a277e3330287fda5ff20a3ca1f78a4 *inst/test/bamFiles/GM12891_POL2_Rep1.bam.bai
a12194d39aeb5b2ebbde87133c18e6dd *inst/test/bamFiles/GM12891_POL2_Rep2.bam
2ae0a12741ac35d0831298e20d98656b *inst/test/bamFiles/GM12891_POL2_Rep2.bam.bai
997d49ae212f74f97a64b01aed6546f6 *inst/test/bamFiles/GM12891_PU1_Rep1.bam
998b4bcdcdb186e1fd5b58d30683f0c5 *inst/test/bamFiles/GM12891_PU1_Rep1.bam.bai
7a22cac3de49546054ef8f8df82a42a4 *inst/test/bamFiles/GM12891_PU1_Rep2.bam
636219877ef28effcd1b244e1bcdab16 *inst/test/bamFiles/GM12891_PU1_Rep2.bam.bai
6233cd0dc9d7c062d13949fc5e77c084 *inst/test/bamFiles/GM12891_TAF1_Rep1.bam
a187811722215c1fd8430933fc38a3d6 *inst/test/bamFiles/GM12891_TAF1_Rep1.bam.bai
c24c39c3f48b953c42348cd4eeeaddd7 *inst/test/bamFiles/GM12891_TAF1_Rep2.bam
df936a76adc86017fb5a5cb03e8d4ac1 *inst/test/bamFiles/GM12891_TAF1_Rep2.bam.bai
2f061f9fa55774118e1bf2a5a1ac963b *inst/test/bamFiles/MCF7_POL2_Rep1.bam
0561c08429e2e8943d35af48c71975e2 *inst/test/bamFiles/MCF7_POL2_Rep1.bam.bai
127547cdd50b20977517f64b929c1373 *inst/test/bamFiles/MCF7_POL2_Rep2.bam
3e9c12865389446af2ec524bcb11c72c *inst/test/bamFiles/MCF7_POL2_Rep2.bam.bai
9dc0992886e0eec82f9c78ae1ed98633 *inst/test/bamFiles/MCF7_STAT3_Rep1.bam
3073b4b11a64775701451e6180910eb4 *inst/test/bamFiles/MCF7_STAT3_Rep1.bam.bai
b0cecc2777ba6181ec9793ebb38bd527 *inst/test/bamFiles/MCF7_STAT3_Rep2.bam
c701a2fcc5c4924daccb6aeed7d7804f *inst/test/bamFiles/MCF7_STAT3_Rep2.bam.bai
08385ed6c2ae1135ca32abcfd82c2ec6 *inst/test/bamFiles/MCF7_cFOS_Rep1.bam
f705cd0ccb3125dbfe19fde5e2a51009 *inst/test/bamFiles/MCF7_cFOS_Rep1.bam.bai
2f2399c06008420a4121f80a9bebb0c7 *inst/test/bamFiles/MCF7_cFOS_Rep2.bam
c5572f6c3713a141646328216b9e346b *inst/test/bamFiles/MCF7_cFOS_Rep2.bam.bai
be47444486cdc2b49dc1cf7162d74b37 *inst/test/bamFiles/MCF7_cMYC_Rep1.bam
43520f9617f87624ed543d6814b1326a *inst/test/bamFiles/MCF7_cMYC_Rep1.bam.bai
0734a720391819ad958f13999556610e *inst/test/bamFiles/MCF7_cMYC_Rep2.bam
ae2ef6b5b4affbd6ff7bcdf863c9deca *inst/test/bamFiles/MCF7_cMYC_Rep2.bam.bai
4c03f33244a44fe39515e6d1bb036df3 *inst/test/bamFiles/TaT1_1.test.bam
fe1dedee858bf49edad20739b5bb1abf *inst/test/bamFiles/TaT1_1.test.bam.bai
d6cc3b916995e4bf48bae8e74e522fe9 *inst/test/bamFiles/TaT1_1_gDNA.test.bam
3748a56f5953699475cd3f21bec30096 *inst/test/bamFiles/TaT1_1_gDNA.test.bam.bai
4f952fb07d1f9e2b740613ea7a210a98 *inst/test/bamFiles/TaT1_2.test.bam
c520097c7d258a1f0b6a5f06141b5993 *inst/test/bamFiles/TaT1_2.test.bam.bai
349667a9277a845fd95ebc190b614608 *inst/test/bamFiles/TaT1_2_gDNA.test.bam
ca3b987727fb4263b84a6bb933abdee1 *inst/test/bamFiles/TaT1_2_gDNA.test.bam.bai
929f55ffc3da8074ab240b76e04d2081 *inst/test/bedFiles/AMOVC_peaks_example.bed
06f98ca796a9f800f28dfb201d4a386c *inst/test/bedFiles/GM12891_PAX5.bed
68597103d71836f6deec44e7dbe1f2d4 *inst/test/bedFiles/GM12891_POL2.bed
116ec66201cde81c531b9708387941b5 *inst/test/bedFiles/GM12891_POU2F2.bed
58726e7f240d620bcbf3be707da2ddb5 *inst/test/bedFiles/GM12891_PU1.bed
d92dd245c5f81dfb0e8635a63026057f *inst/test/bedFiles/GM12891_TAF1.bed
9b41a5263e8b34837bcd6a7ed101d8c9 *inst/test/bedFiles/GM12891_YY1.bed
d035f3fd333747f9d006bdfd39e282e7 *inst/test/bedFiles/MCF7_POL2.bed
abd241e937dc3b71e644684a4422ca75 *inst/test/bedFiles/MCF7_STAT3.bed
fdd7d031d25a131143a6bd5d27c782d2 *inst/test/bedFiles/MCF7_cFOS.bed
1bab8af2bfac63a1ac655346de435642 *inst/test/bedFiles/MCF7_cMYC.bed
6f5c5c4dccbd771660516521f143574a *inst/test/bedFiles/TaT1_peaks_example.bed
53365a0679703dc81ee4a1e1b951d94f *inst/test/exampleChIP.tsv
53365a0679703dc81ee4a1e1b951d94f *inst/test/exampleChIP1.tsv
bb8d4115443b3ef0f6035eb69a851b41 *inst/test/exampleChIP2.tsv
e913c81322ae9dc1e03b32455c017a95 *inst/test/simuloutput/c67c6ec6c433_aln32.bam
d061626a3eb22f7d365c08d31ae6c8c2 *inst/test/simuloutput/c67c6ec6c433_aln32.bam.bai
a1fab3b7b5d897a0699b2abf6468db32 *inst/test/simuloutput/c67c6ec6c433_aln32.fasta
05571db9ed312e90e11b0c3736e86261 *inst/test/simuloutput/c67c6ec6c433_aln32.fasta.sam
2365d78dc6554c234bdff66cb7cd75c4 *inst/test/simuloutput/c67c6ec6c433_aln32_snplist.txt
05ac5211662361082559cb329a47e5a7 *inst/test/simuloutput/c67c6ec6c433_aln34.bam
8b5e3a044dd05dfb92fb8db7fde3ff71 *inst/test/simuloutput/c67c6ec6c433_aln34.bam.bai
a5b675819f83fe2c0df8a7413a76feb6 *inst/test/simuloutput/c67c6ec6c433_aln34.fasta
9399ebfb7dc77fd0f55ead28f7277684 *inst/test/simuloutput/c67c6ec6c433_aln34.fasta.sam
b71ba0d4c0ab066b48f80663f53f5309 *inst/test/simuloutput/c67c6ec6c433_aln36.bam
c43a70ce0f97d7a193804558ce7801f9 *inst/test/simuloutput/c67c6ec6c433_aln36.bam.bai
f142dec4a976b5abe0acaaa5089def56 *inst/test/simuloutput/c67c6ec6c433_aln36.fasta
237245fd81664a1fe42cf8474c1b4f77 *inst/test/simuloutput/c67c6ec6c433_aln36.fasta.sam
18bac19354572692976bcc91e61b7118 *inst/test/simuloutput/c67c6ec6c433_snplist.txt
78e0e36e57a587d0fa71f43259726e34 *inst/unitTests/test_get_allele_counts.R
1e2cbdef22acc35554f434b2a2632c54 *man/BaalChIP.Rd
c47fbd9269cba5f89df67cbda1ecd77c *man/BaalChIP.get.Rd
c210228d0ae8a5e4937157c1201b00c5 *man/BaalChIP.report.Rd
52715f42279e78f38333d12fe5a467a0 *man/BaalChIP.run.Rd
7e207ded05fca6f457d94a474d4a7b9f *man/BaalObject.Rd
84a9973ff6b77e87f823ed27e37b0199 *man/ENCODEexample.Rd
60859c42ac40ea34054861676c621cb7 *man/FAIREexample.Rd
d675bebcb7adfe903b202b4d219e07d2 *man/QCfilter.Rd
c31203041bfad891084a202ae42309f3 *man/UniqueMappability50bp_hg19.Rd
9b200a42cdbdb70cb172aa322532316a *man/adjustmentBaalPlot.Rd
61dae3fd8bffaf26a1920af12b783a42 *man/alleleCounts.Rd
b16cff41729fbb6143c71da9b95711ac *man/blacklist_hg19.Rd
fd4b22aa99c9cf8ac922ad4f3b73f47f *man/filter1allele.Rd
12cc9e07947b984b99bfe31b7be21ae1 *man/filterIntbias.Rd
64cc2a50df74b6c8980d1bffb3e964ae *man/getASB.Rd
df15af03629e67d63294c0fd593c4485 *man/mergePerGroup.Rd
716afd83df234081a86a4c6ede298fe5 *man/pickrell2011cov1_hg19.Rd
4eab615e5637b5d814522bbbd68f63c9 *man/plotQC.Rd
d7cd9bc7d762c327f6c4076dadda2a61 *man/plotSimul.Rd
5462ab3434c71a46d11f918fb9843c6f *man/summaryASB.Rd
1269d76345f0b87c658a1d1f95d47c08 *man/summaryQC.Rd
c697f6f160e82f25a86d3a2bda81e2a7 *tests/runTests.R
5ba44acbd1c5c845bfd1075a108e5c0c *vignettes/BaalChIP-vignette.bib
d150e9563a6eaff6465ff1abb9fa974c *vignettes/BaalChIP.Rmd
331d5802da7e8d036a0ae98998cf9b41 *vignettes/baal.png
a9af0df8592b7f97997c09bcf8aaed45 *vignettes/biomed-central.csl
