814be67e5c247e2ea6e0e11f4765ccbb *DESCRIPTION
c795dc8ca6ff2887ab424599ad44a21e *NAMESPACE
a18429026f52165cdb6fdb05d537d8e2 *NEWS
df1cd24e40714bbfcf60398ee8661e0d *R/Class_AlignedData.R
c82547ca8b26e4fe59b8f262a8e2de4c *R/WigRepeatAnalyzer.R
bd3f4c08b3842008a7c33e50b2b54505 *R/binVector.R
9679d127d6df94081431b983f2783c55 *R/elongationEstimation.R
cdb7d46d6276cc866718ec4f2a00197e *R/mergeWigs.R
0c3bc2684bbf2bccab2fd7af2bf96e67 *R/multiread_CSEMDispatch.R
885a171100c102e23d068c69cd19fc88 *R/multiread_RemoveArtifact.R
869df11366aa15ef930c26934f6b407b *R/multiread_UniformDispatch.R
6ed6002084e219194214b36ea5e7e438 *R/normAndSubtract.R
766568fd6c7d7df3759883fb3db90f4b *R/pileupDouble.R
0671bfb64b03ff1ef668026f8cae3d6c *R/pipelineChipSeq.R
f6a43e4d7f4d57376adb57b6739decd7 *R/plotReadsRepartitionAnnotations.R
b41e52cf1625477dc685f3b180823054 *R/readAlignedBAM_minimalSEQ.R
c37debf35febd542d0f19ddac8da7a73 *R/test_functional.R
d9bee72d6518858932888cdba318f411 *R/test_functional_multiread.R
9fa7d1722dbb8afe348d49eb837969f1 *R/wigIO.R
106e5e944f06d68dbbaf67e728247304 *build/vignette.rds
efac075dce78d8cdd5b46300083f77a2 *inst/doc/Pasha.R
1c9af25d66486eae80e20d4d8adf7a45 *inst/doc/Pasha.Rnw
e4ff109a53b5c0c87e93f8f33e47f328 *inst/doc/Pasha.pdf
887150c8e7a9922d50fa78a1cfd6af7d *inst/extdata/embedDataTest.bam
d6201f589d810b79abea4e60acc1d67a *inst/extdata/embedDataTest.bam.bai
3ef1cc06ae36a289af54d2ae18e0f4f1 *inst/extdata/embedDataTest.sam
f197bfcc38e6c20033af609af7422d00 *inst/extdata/embededDataTest_MultiSignal.bow
8333989901b78e1cf45bd6ec674fa3a2 *inst/extdata/embededDataTest_MultiSignal.txt
f6a5e9f794b212f25d2393ba09037a35 *inst/extdata/mm9_RepeatMasker_2000l.txt
3de369e12edf24806a1ef713d23b197e *inst/extdata/resultTests.pdf
4a58d73341c2d85572a29d19af17b321 *inst/extdata/resultsFromFunctionalTestsWIG.tar.gz
51504e66019ea67312224f6fc58bf46b *inst/extdata/resultsFromMultireadFunctionalTests.tar.gz
1a7a8ed0edd8e067a7ac26d93ffec2d2 *inst/resources/ce10.ref
d70e6c7982948d4ea655f02cf020d268 *inst/resources/dm3.ref
1ea9e83ed30353a91f0df23d355292d4 *inst/resources/hg18.ref
d968d89d6d5d5a10b9272d304f58b707 *inst/resources/hg19.ref
7e1169dc44ff95b6c437b9a56f4244b9 *inst/resources/mm9.ref
5a204a21dfa5cd432c3e2d32dfa36e28 *inst/resources/sacCer3.ref
e1c8742c968cb190cc536a7e80e38812 *man/AlignedData-class.Rd
ed05604eea4fd62892d18c1e0ae96b31 *man/PASHA-package.Rd
bfc58580b5071d785dcd8e63bf011104 *man/WigRepeatAnalyzer.Rd
ca247cb0b32da3deab350e2a703cf8cf *man/binVector.Rd
0fe5c9553899e264eb718c1ddb269156 *man/elongationEstimation.Rd
3153d93ee3997803e8206b12c2be1d44 *man/estimateElongationSize.Rd
506a6dab32d39de65e3363f32d5ceaf2 *man/generatePiled.Rd
dfd7866bbbd82790e44e6a0b4a560b52 *man/getArtefactsIndexes.Rd
5cc4f2fa98aaa8f269bfe6a1264361f8 *man/mergeWigs.Rd
a4d195246f86c238c9e63d10d61cbaa1 *man/multiread_CSEMDispatch.Rd
38721ef8819dd7303861fb50d1b2f4cb *man/multiread_RemoveArtifact.Rd
cf88c14bc1d7a006be26639bd3822aeb *man/multiread_UniformDispatch.Rd
0901f4ce34da93b005cd54c6971cd360 *man/normAndSubtract.Rd
887162a8fa89f939f0e7e35ea0c024f4 *man/pileupDouble.Rd
947adf3637dd37afdbcdfa9ac17d0a79 *man/plotReadsRepartitionAnnotations.Rd
4d13e93a4223341dbb9577184bde08a7 *man/processPipeline.Rd
5ce4ec652e424529bf4c02f7fcefa038 *man/testFunctional.Rd
73eab91d14834f4f05e9ea5b04999936 *man/testMultireadFunctional.Rd
7dcc269cfa24a5cb39f1cb6329471239 *man/wigIO.Rd
f60f4e7274e54ab7da2dd11c84e47b49 *src/AlignedTag.cpp
8405741b8e6f9d732b10d402798005a6 *src/AlignedTag.h
c7e9f5526520588bd92f21543b44b029 *src/MultireadArtifactRemover.cpp
52fc358b3eace6c081b1201ba0ed36c0 *src/MultireadArtifactRemover.h
4ff4815dea73e829a8f9ea6f1ecd5ac4 *src/MultireadArtifactRemoverMain.cpp
33df61c18da3df4adf9d23da022c578f *src/MultireadCSEMBcTree.h
0a69649a412fbace200b0c530e1effdd *src/MultireadCSEMDispatcherMain.cpp
7943e3fb95b01ae6c24584592b0561dd *src/MultireadCSEMPosPair.h
7ba2502a6faf2fe489209c385023dbd4 *src/MultireadDispatcher.cpp
365d531348e8462f67d72cd29d678a3f *src/MultireadDispatcher.h
cfb9103e48c485f184bd4b6cf6844175 *src/MultireadDispatcherMain.cpp
a387b35162707984bca12c1e6594a717 *src/R_init_Pasha.c
e8e36af78e25eab5431f30a1248b8a6d *src/RepeatLocus.cpp
436f1fb4d3dcbdf2e1fb74095d9a114e *src/RepeatLocus.h
0c5e22416dbf1f335722b560e6f0dfdc *src/WigLocus.cpp
e1d77d794da76ce5573f7e49114aba26 *src/WigLocus.h
e2f1008085f605806b26de6fc3ce7f87 *src/WigRepeatAnalyzer.cpp
1441d44ad1300e3de55586f5e64737e6 *src/WigRepeatAnalyzer.h
4883c989f65e6de46277a40bcfc843c9 *src/WigRepeatAnalyzerMain.cpp
6a41294862929ad3b7e0e97c82ec9ecb *src/binVector.c
38745b8cf7cc1c67960b29ebc7ff0587 *src/elongationEstimation.c
484e877ab0a6f73078d6c2b67139bf94 *src/pileupDouble.c
98a7feb0b512e9a89aab0f55d874a5bb *src/regex.h
474535c6d68ba253d1eb66b92a688b45 *tests/test_Pasha.R
31220bcea5e59616c9ef622bacbfc215 *tests/test_Pasha.Rout.save
1c9af25d66486eae80e20d4d8adf7a45 *vignettes/Pasha.Rnw
