486f088abeea2c26fc3fbb68aac5f223 *DESCRIPTION
1b45c26aae1f931379e5d33e7480f82c *INDEX
4b4285b0168122e3cde4cf19bc0d5c91 *Meta/Rd.rds
1ef47c04e418598929af15afced20d9d *Meta/data.rds
a4081712be3649fee57cb72b810cc0f9 *Meta/features.rds
d4ee44ad7cc13e304e03368a7caef432 *Meta/hsearch.rds
fa0a964b58849a023808276102875f3c *Meta/links.rds
24a71c46108bde5721cee8fb8376205f *Meta/nsInfo.rds
265eb13b2a46953bc750683ee94a4305 *Meta/package.rds
c0ac9a67c81131c46fc6f4effb722008 *Meta/vignette.rds
8266d81f797b7c152fca7d2d0b62780f *NAMESPACE
6e413c2bcd6660a83f0ffad53dcd0d54 *NEWS
ebf0fc819595d631b8bf280c4b049940 *R/BaalChIP
fbc6000ebfb352871255aac49ae78165 *R/BaalChIP.rdb
1034588ec77e6288ad68f972cc011f05 *R/BaalChIP.rdx
e174b7711c3f24e96d7ed3d2f0cd9315 *data/Rdata.rdb
f97824f855a9120c23af2cedeead2613 *data/Rdata.rds
86c12d9f3b8b10a9cb464b60298ea8cb *data/Rdata.rdx
238836dcba18728bd32c69aa762eca44 *data/datalist
3ed1caded7e1e53d76235b43f894722e *doc/BaalChIP.R
218493e6b88be988640a5421a7aafdbc *doc/BaalChIP.Rmd
52d72c382f6a895a7b5421367ea8a87e *doc/BaalChIP.html
a0cd49b193285b36eff89c7c1cf739b5 *doc/index.html
f3740b5b23040b009ef3773971635469 *extra/get.overlaps.v2_chrXY.perl
2839f9d957e8408f360a73c807dc577d *extra/run_simulations.sh
60a5dd8af3212a3cb7f2ec05d2a1c161 *help/AnIndex
86ff1b8ede0893989eeace8a2216e716 *help/BaalChIP.rdb
296b7f6258bb3897b07c9ee4369a27ca *help/BaalChIP.rdx
26429b7ddf2e14bed633eb794a1c732c *help/aliases.rds
8a0999e131e65dca34bf186b03b0d14b *help/paths.rds
235e0276f910ebf3d54d38c6f319a5c5 *html/00Index.html
79944369fb420dc901c8807822f184e6 *html/BaalChIP.get.html
969c77f223471e607e0e18c8c99b19fb *html/BaalChIP.html
1a87125767841a1a184c001c21acc454 *html/BaalChIP.report.html
03d4859b5dc85cfc43dbdeb17fd5dbd3 *html/BaalChIP.run.html
a95eef2fe149fcfccab2ea42a8a4e496 *html/BaalObject.html
470f335f5749c1a944138770890f8825 *html/ENCODEexample.html
f70e6964462586d695e780f3588f6885 *html/FAIREexample.html
1383edfcdbf9c1147b25fe951c6c2083 *html/QCfilter.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
352e29e8345c2613a0b21caa503673d7 *html/UniqueMappability50bp_hg19.html
6fde4e9623af1cc300e930d78ff3be95 *html/adjustmentBaalPlot.html
68c7f8fd9ad68e616785a3661d1f5a9d *html/alleleCounts.html
5fe52bf0cce312d5df6c3c924794666a *html/blacklist_hg19.html
972aabf496ad9b062a9295bf4a3dad4e *html/filter1allele.html
ddb1b915309ad2c91ed84c8996aec2e6 *html/filterIntbias.html
c6ee48c480fc7d48513af48bc65c2205 *html/getASB.html
9211c034a7da8d0dcf26b46382ce23e1 *html/mergePerGroup.html
e14708830cdc44ab6de25083ee6452eb *html/pickrell2011cov1_hg19.html
39be3bb22af32b799986feb56bec2960 *html/plotQC.html
b3273d552012afc8da7e0140df2b50e3 *html/plotSimul.html
09cef9267a03d990afbc5648b59d92bc *html/summaryASB.html
cfde46816d8ef8ed2b02adc40950264f *html/summaryQC.html
aef76ff89c48aba2836b3513c48f19f7 *test/AMOVC_hetSNP.txt
6f96297112143141b7722d1d8e1fd20d *test/GM12891_hetSNP.txt
14febf61389ef198586e9074ba9eaca8 *test/MCF7_hetSNP.txt
c1be60bd8936a53b079829368f57d76c *test/TaT1_hetSNP.txt
49acfc2455f48ad0190affee3372a634 *test/bamFiles/AMOVC_1.test.bam
1c1cc28d69259e2c87422d61205f539b *test/bamFiles/AMOVC_1.test.bam.bai
f67f8ecb8ea2d66c30a1122a826a6af8 *test/bamFiles/AMOVC_1_gDNA.test.bam
d18eba452a93662a289675442e94f1f5 *test/bamFiles/AMOVC_1_gDNA.test.bam.bai
6d5bf9cfd0dedeedef41bfd5443fb5d6 *test/bamFiles/AMOVC_2.test.bam
be60f1e7b165c1c1d0652e9ffd679c9e *test/bamFiles/AMOVC_2.test.bam.bai
b3ce873d07f0e6ae99abb9d9b6ecfe3c *test/bamFiles/AMOVC_2_gDNA.test.bam
128b4d27f35763fc65bc44cbc45ac902 *test/bamFiles/AMOVC_2_gDNA.test.bam.bai
028c88d8fb7fef3f0442989943a78e51 *test/bamFiles/GM12891_PAX5_Rep1.bam
17324b40c7882848277978bedc306465 *test/bamFiles/GM12891_PAX5_Rep1.bam.bai
f5e867bdc8995501db93f171735c3f68 *test/bamFiles/GM12891_PAX5_Rep2.bam
0ff0682341c9144b5daee17c44edcb47 *test/bamFiles/GM12891_PAX5_Rep2.bam.bai
91983547913597ab2053ab19fe64a248 *test/bamFiles/GM12891_POL2_Rep1.bam
61a277e3330287fda5ff20a3ca1f78a4 *test/bamFiles/GM12891_POL2_Rep1.bam.bai
a12194d39aeb5b2ebbde87133c18e6dd *test/bamFiles/GM12891_POL2_Rep2.bam
2ae0a12741ac35d0831298e20d98656b *test/bamFiles/GM12891_POL2_Rep2.bam.bai
997d49ae212f74f97a64b01aed6546f6 *test/bamFiles/GM12891_PU1_Rep1.bam
998b4bcdcdb186e1fd5b58d30683f0c5 *test/bamFiles/GM12891_PU1_Rep1.bam.bai
7a22cac3de49546054ef8f8df82a42a4 *test/bamFiles/GM12891_PU1_Rep2.bam
636219877ef28effcd1b244e1bcdab16 *test/bamFiles/GM12891_PU1_Rep2.bam.bai
6233cd0dc9d7c062d13949fc5e77c084 *test/bamFiles/GM12891_TAF1_Rep1.bam
a187811722215c1fd8430933fc38a3d6 *test/bamFiles/GM12891_TAF1_Rep1.bam.bai
c24c39c3f48b953c42348cd4eeeaddd7 *test/bamFiles/GM12891_TAF1_Rep2.bam
df936a76adc86017fb5a5cb03e8d4ac1 *test/bamFiles/GM12891_TAF1_Rep2.bam.bai
2f061f9fa55774118e1bf2a5a1ac963b *test/bamFiles/MCF7_POL2_Rep1.bam
0561c08429e2e8943d35af48c71975e2 *test/bamFiles/MCF7_POL2_Rep1.bam.bai
127547cdd50b20977517f64b929c1373 *test/bamFiles/MCF7_POL2_Rep2.bam
3e9c12865389446af2ec524bcb11c72c *test/bamFiles/MCF7_POL2_Rep2.bam.bai
9dc0992886e0eec82f9c78ae1ed98633 *test/bamFiles/MCF7_STAT3_Rep1.bam
3073b4b11a64775701451e6180910eb4 *test/bamFiles/MCF7_STAT3_Rep1.bam.bai
b0cecc2777ba6181ec9793ebb38bd527 *test/bamFiles/MCF7_STAT3_Rep2.bam
c701a2fcc5c4924daccb6aeed7d7804f *test/bamFiles/MCF7_STAT3_Rep2.bam.bai
08385ed6c2ae1135ca32abcfd82c2ec6 *test/bamFiles/MCF7_cFOS_Rep1.bam
f705cd0ccb3125dbfe19fde5e2a51009 *test/bamFiles/MCF7_cFOS_Rep1.bam.bai
2f2399c06008420a4121f80a9bebb0c7 *test/bamFiles/MCF7_cFOS_Rep2.bam
c5572f6c3713a141646328216b9e346b *test/bamFiles/MCF7_cFOS_Rep2.bam.bai
be47444486cdc2b49dc1cf7162d74b37 *test/bamFiles/MCF7_cMYC_Rep1.bam
43520f9617f87624ed543d6814b1326a *test/bamFiles/MCF7_cMYC_Rep1.bam.bai
0734a720391819ad958f13999556610e *test/bamFiles/MCF7_cMYC_Rep2.bam
ae2ef6b5b4affbd6ff7bcdf863c9deca *test/bamFiles/MCF7_cMYC_Rep2.bam.bai
4c03f33244a44fe39515e6d1bb036df3 *test/bamFiles/TaT1_1.test.bam
fe1dedee858bf49edad20739b5bb1abf *test/bamFiles/TaT1_1.test.bam.bai
d6cc3b916995e4bf48bae8e74e522fe9 *test/bamFiles/TaT1_1_gDNA.test.bam
3748a56f5953699475cd3f21bec30096 *test/bamFiles/TaT1_1_gDNA.test.bam.bai
4f952fb07d1f9e2b740613ea7a210a98 *test/bamFiles/TaT1_2.test.bam
c520097c7d258a1f0b6a5f06141b5993 *test/bamFiles/TaT1_2.test.bam.bai
349667a9277a845fd95ebc190b614608 *test/bamFiles/TaT1_2_gDNA.test.bam
ca3b987727fb4263b84a6bb933abdee1 *test/bamFiles/TaT1_2_gDNA.test.bam.bai
929f55ffc3da8074ab240b76e04d2081 *test/bedFiles/AMOVC_peaks_example.bed
06f98ca796a9f800f28dfb201d4a386c *test/bedFiles/GM12891_PAX5.bed
68597103d71836f6deec44e7dbe1f2d4 *test/bedFiles/GM12891_POL2.bed
116ec66201cde81c531b9708387941b5 *test/bedFiles/GM12891_POU2F2.bed
58726e7f240d620bcbf3be707da2ddb5 *test/bedFiles/GM12891_PU1.bed
d92dd245c5f81dfb0e8635a63026057f *test/bedFiles/GM12891_TAF1.bed
9b41a5263e8b34837bcd6a7ed101d8c9 *test/bedFiles/GM12891_YY1.bed
d035f3fd333747f9d006bdfd39e282e7 *test/bedFiles/MCF7_POL2.bed
abd241e937dc3b71e644684a4422ca75 *test/bedFiles/MCF7_STAT3.bed
fdd7d031d25a131143a6bd5d27c782d2 *test/bedFiles/MCF7_cFOS.bed
1bab8af2bfac63a1ac655346de435642 *test/bedFiles/MCF7_cMYC.bed
6f5c5c4dccbd771660516521f143574a *test/bedFiles/TaT1_peaks_example.bed
53365a0679703dc81ee4a1e1b951d94f *test/exampleChIP.tsv
53365a0679703dc81ee4a1e1b951d94f *test/exampleChIP1.tsv
bb8d4115443b3ef0f6035eb69a851b41 *test/exampleChIP2.tsv
e913c81322ae9dc1e03b32455c017a95 *test/simuloutput/c67c6ec6c433_aln32.bam
d061626a3eb22f7d365c08d31ae6c8c2 *test/simuloutput/c67c6ec6c433_aln32.bam.bai
a1fab3b7b5d897a0699b2abf6468db32 *test/simuloutput/c67c6ec6c433_aln32.fasta
05571db9ed312e90e11b0c3736e86261 *test/simuloutput/c67c6ec6c433_aln32.fasta.sam
2365d78dc6554c234bdff66cb7cd75c4 *test/simuloutput/c67c6ec6c433_aln32_snplist.txt
05ac5211662361082559cb329a47e5a7 *test/simuloutput/c67c6ec6c433_aln34.bam
8b5e3a044dd05dfb92fb8db7fde3ff71 *test/simuloutput/c67c6ec6c433_aln34.bam.bai
a5b675819f83fe2c0df8a7413a76feb6 *test/simuloutput/c67c6ec6c433_aln34.fasta
9399ebfb7dc77fd0f55ead28f7277684 *test/simuloutput/c67c6ec6c433_aln34.fasta.sam
b71ba0d4c0ab066b48f80663f53f5309 *test/simuloutput/c67c6ec6c433_aln36.bam
c43a70ce0f97d7a193804558ce7801f9 *test/simuloutput/c67c6ec6c433_aln36.bam.bai
f142dec4a976b5abe0acaaa5089def56 *test/simuloutput/c67c6ec6c433_aln36.fasta
237245fd81664a1fe42cf8474c1b4f77 *test/simuloutput/c67c6ec6c433_aln36.fasta.sam
18bac19354572692976bcc91e61b7118 *test/simuloutput/c67c6ec6c433_snplist.txt
78e0e36e57a587d0fa71f43259726e34 *unitTests/test_get_allele_counts.R
