1ccd7fe2aaf9f6a05bec678ac884fe7e *DESCRIPTION
84dcc94da3adb52b53ae4fa38fe49e5d *LICENSE
e577d9ef4009bd1c47d06f93d0516ab4 *NAMESPACE
2c911da9c5c6c777ac00d014c23ed678 *R/ATACProc.R
f17fc1246ac7d945aa5cf68e092d90de *R/BamToBed.R
4c6ff60c24f691c4547985f262ec9fe1 *R/BedToBigWig.R
19cbaad6bb9b9789f4c8b02b340b3c81 *R/BedUtils.R
e7d34111969bd82b0e251f7b4cca68cc *R/ConfigVal.R
150f4167c80f3980f8e8b7ed27dcbb9a *R/CppInterface.R
79733f66c8d1450cc27d9624b3afe746 *R/CutSiteCountR.R
f82c00f4732a86e07098360627e3d039 *R/CutSitePre.R
37e307892b5aea05396471fc4ca128c5 *R/FRiPQC.R
72bc6829720b7be1aad59ee6b44df427 *R/FastQC.R
58e041621e73dba8471f21b80e7320ad *R/FindAdapter.R
2ecf51f1676e5bb9c31ac617ed893070 *R/FregLenDistribute.R
21b7ac64f47ad0a0786cb19f5641b4e8 *R/JavaExports.R
f018288023735602f851de1f67734cb0 *R/JavaInterface.R
0b4ff34d2ae1f0381992332f53764ab7 *R/LibComplexQC.R
71b55bb5035ba902291b9cb271f60fc9 *R/Mapping.R
25776d31d6f2d723406b3c6eab4259e1 *R/Methods.R
f1a09110e42a64add97f5e085399902e *R/PeakCallingFseq.R
ec5118e177675b83c252a39c73169a96 *R/PeakCallingMACS2.R
79e7d57f1d192efd9c861ed45cf0cc86 *R/PeakQC.R
90dcc93cb2feb6cb6c5d184be0294fbd *R/RGo.R
b7963f730427945b256697a90b4075b8 *R/RMotifScan.R
af33335790f505cf93c00b1b8e2c2906 *R/RMotifScanPair.R
f6e6fbafd3452d2e8ff39c52fe1ddb0e *R/RPeakAnno.R
a6454d2002960f24a53c798417dfd786 *R/RPeakComp.R
48b1f06568a8f1f57255f5b55fce26d4 *R/RSNPs.R
ff439b94ab5d82e84a36c4f04703484e *R/RcppExports.R
b811bf8e5a9ce05571289fd6251c5fa8 *R/RemoveAdapter.R
2095a40cb37c26c86b39158c7f54ca10 *R/Renamer.R
5dfe27f0e4d4962149e29a635da7042b *R/Rsortbam.R
b48f6fa968bdb86aa7450e2087e86bb7 *R/SamToBam.R
cecdb351ad0d251692fa62704890736e *R/SamToBed.R
02495229c02a6a28dc1b0a4fbdae3561 *R/SingleRepReport.R
d445af283d6dfec426e19ab956086396 *R/TSSQC.R
c3264277061229eb2745b03ab457e7d1 *R/UnzipAndMerge.R
4c9714d6bfb8a33a28112bf07d3f3aad *R/onLoad.R
5566824bba96bf21e270cdcbbe99000b *R/utilities.R
e9f9c61bc9a3bc6dde42c07ba07bff4f *build/vignette.rds
e7c87cbb6173edfea2e59a60cbacad76 *inst/CITATION
c347a6c6982c09fdcc21b0f303264b45 *inst/NEWS
f1cd6c0130baecaf7bd69d9af086a244 *inst/doc/esATAC-Introduction.R
8e23fbe723cc04978ce63ae7f57380a4 *inst/doc/esATAC-Introduction.Rmd
bfd1c04947591046cdb6e05140decf88 *inst/doc/esATAC-Introduction.html
36743e99f29d61bd236bfb0de1494e52 *inst/extdata/CustomizedMotif.txt
3f2358b92a1a92db4c219a5ce642bbfa *inst/extdata/Example.sam.bz2
abed1938fb2f2008207c1e58134aa8d1 *inst/extdata/Example_peak1.bed.bz2
94a7776ecdd7a21959667efea87e798b *inst/extdata/Example_peak2.bed.bz2
c7be260d03ee691324497b0012046464 *inst/extdata/MotifPFM.rds
8a138c786b2070d895068d68fc23a73c *inst/extdata/Rep_Report.Rmd
136257b71598d9f77b45249308fbe0d1 *inst/extdata/Rep_Report2.Rmd
7e53d316fea8aea2d90399d732de9dcd *inst/extdata/Rep_Report_Index.Rmd
9ab7a11ee72d721003af3f18c568dd0d *inst/extdata/Report.Rmd
d2d8c164ea5817561578e3affa20da02 *inst/extdata/Report2.Rmd
6d2dc573b517f3ae445be66a6a881a6e *inst/extdata/Report_Index.Rmd
5c73c832edec2c7cc5fa382cca64c73b *inst/extdata/basicReport.Rmd
163f1b0ead6962e41a18bb2ccc5149ba *inst/extdata/bt2/reads/reads_1.fastq
a0529d01ceb200399b8d6fb703cc51f1 *inst/extdata/bt2/reads/reads_2.fastq
d9cd45a2cfd805f55eea9b7ddc76233e *inst/extdata/bt2/refs/lambda_virus.fa
56d15ee18a2ababff9fa9aa66b00da21 *inst/extdata/chr20.50000.bed.bz2
0ba127b8f969bb28a39acfadaf7bccaa *inst/extdata/chr20_1.1.fq.gz
f9999fe9ab57b3882370615e574edc87 *inst/extdata/chr20_1.2.fq.bz2
b0b53566e020d619aa8b6c0b068e23ec *inst/extdata/chr20_2.1.fq.gz
c5d1b5d488187eaf8d0f572e07273733 *inst/extdata/chr20_2.2.fq.bz2
6ebd808795a9543e547aa25c08248de3 *inst/extdata/chr20_sample_peak.bed.bz2
88d1b2ca688e7a402317d82853da4dbd *inst/extdata/hg19.blacklist.bed
eedf14c6c49c62aa6befba57d5fd13ca *inst/extdata/snp_info
2dfb8dfb1073db7615cb166c818683c7 *inst/extdata/uzmg/m1/reads_1.fastq.1.bz2
09626db4095d7c8bf3c1a034e4d81771 *inst/extdata/uzmg/m1/reads_1.fastq.2
117f7c0e898df75cdbfedf5510a6a930 *inst/extdata/uzmg/m1/reads_1.fastq.gz
cb9a8c465a0ae9427beb1bd428a1650d *inst/extdata/uzmg/m2/reads_2.fastq.1.bz2
30f0ba5ca995e1cb1402a8d25fcaae7a *inst/extdata/uzmg/m2/reads_2.fastq.2
be85283f2a8033100a56a320be3c56e1 *inst/extdata/uzmg/m2/reads_2.fastq.gz
b91e43d736c9013512f049c3cecb9fd7 *inst/java/commons-cli-1.1.jar
356b525e390ee9c6ffb800c390790e25 *inst/java/fseq.jar
5d314be0bb34c5bd5962c05de74fb8ca *man/ATACProc-class.Rd
ce2b6304cc1186d2dc73c30aaaa06029 *man/BamToBed.Rd
a44854c1edb49197dbb2955528e1f6d7 *man/BedToBigWig.Rd
a2387d5144b43f0a01521a69da710f8c *man/BedUtils.Rd
738311e47271fc9142a40be2f7895839 *man/Bowtie2Mapping.Rd
ae0c3451dce180e14c9e663ae06f6867 *man/CutSiteCountR.Rd
970e2d2a6f8ebfd56c42d22e959c0249 *man/CutSitePre.Rd
4a24dbfd239fceb06b3e981b1b849631 *man/FRiPQC.Rd
fb59097d4ee55e31f361ad5751b48be9 *man/FastQC.Rd
c0d6ac10b8e2894b17208f130dedf199 *man/FindAdapter.Rd
b64543a25103e2bd6016764358df03d3 *man/FragLenDistr.Rd
53c786b052aa14c5022328c96c455733 *man/LibComplexQC.Rd
deb2bd8f785ee972a12253c7e29308dd *man/PeakCallingFseq.Rd
d0e50c9e81e39bf13a3196121b6988a8 *man/PeakCallingMACS2.Rd
ea34781b8ceae3f5e6133050489eba91 *man/PeakQC.Rd
245474fa95a3d743a2f099381999ebe2 *man/RGo.Rd
eae1bad4b931385c26cc66d24959844c *man/RMotifScan.Rd
a74f342c2c8248d39bc1de939ccb03cb *man/RMotifScanPair.Rd
de2e16965422fa507f7c89f1c67cdab1 *man/RPeakAnno.Rd
1cd446ffaa283c09ee3c8f1d8e4161e3 *man/RPeakComp.Rd
fa40d2ff175829508e86bfe0bf4e8de9 *man/RSNPs.Rd
3b38721e2d3f11aef392309f24e52a03 *man/RemoveAdapter.Rd
efcc643437c488e2137a9509fc338eb2 *man/Renamer.Rd
ad175b31d80ed9bbce44dfde3bfe77fe *man/Rsortbam.Rd
9ffa5e3870798adf4a89e05b4cf76d21 *man/SamToBam.Rd
7fed0724d7c5d56fc1e0cc38be9fe963 *man/SamToBed.Rd
2def7c29ef9b430415c3975672d62c7f *man/SingleRepReport.Rd
02139286a9ef713a0a1d7f4635d3523e *man/TSSQC.Rd
beee20b64e8918a74fa0f9f4b41a9857 *man/UnzipAndMerge.Rd
09c05c565316e6b9e95ceafe03144805 *man/atacPipe2.Rd
ff5bf9f3c61a7c4c2ee68f242f65743a *man/atacRepsPipe.Rd
a2f93a4d1358227210674d2c9c10ff71 *man/atacRepsPipe2.Rd
5c6e15dcb8579dfacd3d0ed86dedd6b3 *man/esATAC-package.Rd
206025d4f7cfa7e932e67aeb02697b48 *man/getMotifInfo.Rd
c6925294d73e9518ec04301c1a10e04a *src/BedLine.cpp
63d75f5e2abb02ae6f0f215506074f4e *src/BedLine.h
7c88aa38cc6f75834471de0f0391f259 *src/BedUtils.cpp
3853fb32cccbadc2902d4ceb3aa63098 *src/BedUtils.h
b2f500ce34845b57df6401a2c585f50a *src/ChrDivi.cpp
37a6eff0873ca6cb64551afcd8a27023 *src/ChrDivi.h
16d082bc73a1a9dcf08408d5b764ecc0 *src/CutCountPre.cpp
c9ce1a1c77cb2782fb2b729c76a6088f *src/CutCountPre.h
a3ff3cba7cf08e0bc8b740264055b794 *src/CutSiteCount.cpp
6215a3365a0bb6978235083743505609 *src/CutSiteCount.h
b8c2421f427388ac811198e02b6e60ae *src/LibComplexQC.cpp
43ad9e5c20730ed880bccdf191dc42da *src/LibComplexQC.h
60a37883107406d0e68008915db8d444 *src/Makevars
a74cbcf407f082aceb7dee322f6069c7 *src/Makevars.win
f67a9d78c86f646fbe54a2de46c75025 *src/RcoutRcerr.h
802dc6f3fbeceb8759e1aecc513ed70f *src/RcppExports.cpp
e2f245927bb44c84477c7310058bd0b4 *src/SortBed.cpp
5602c58161d75697331b08e632bcae60 *src/SortBed.h
b61d24b3dd211e24f3004f0c3d213500 *src/rcpp_wrapper.cpp
7c265a39ec5543cdcf77f9f824f36f62 *src/renamer.cpp
4fd5ecb7b79d3e373efc1ca84ffd4047 *src/renamer.h
eb28f359cdfedfd74228c4b407e0fc4f *src/sam2bed.cc
0247729762bbedcbd82bd50f01971562 *src/sam2bed.h
2256ae64a3c6b2454748f2f0d0fbef39 *tests/testthat.R
2a2cde7d085931c713966a86e712db4f *tests/testthat/test-basicopr.R
8e23fbe723cc04978ce63ae7f57380a4 *vignettes/esATAC-Introduction.Rmd
004f704ff9cf63483be2058202466140 *vignettes/whole.png
