f05aed2ff2ca7ab9b6cc0520e933424c *DESCRIPTION
29a9012941a6bcb26bf0fb4382c5dd75 *LICENSE
d16a08dcb01db5d9628367e8ce4e09a0 *NAMESPACE
244cb7d24d4f3b9d0ce903bd166bf32e *NEWS
58c0b9b7e16a965f0d3fc7c66ab10558 *R/AllClasses.R
b9c0d17721f9b413d313e11864aedeb9 *R/AllGenerics.R
f14ebed39bbd95029f662a36857917dc *R/annotateTSS.R
8ef492dbd4a48d0a0ebd247e537d91d5 *R/demultiplexFASTQ.R
2441d7ccff9c1de53c3291e52ca0e3cf *R/detectDiffTSS.R
441d8c56ec21529acaa16e348e00d51d *R/detectTSS.R
a20ae7acea29376ff52bceb7c24e48be *R/exampleCSobject.R
2d17035f8e587b195c3a11c99b6c3931 *R/filterDuplicates.R
2b5250ad0c0bcd0d0a51d2664fdada55 *R/getGeneCounts.R
9469465e39bfd086d92d6b9e64dd069c *R/mapCaps.R
b18791e01d1ae7d40dfa56dd8e1d2fde *R/methods.R
a84455afcf3cb42645e0dbb7609b9c2b *R/plotting_functions.R
2c1758571f45aeff24c72511288f2d3c *R/splitBAM_byIndex.R
1614032025c38519bba6a67e2e5e71c9 *R/splitBAM_byRepindex.R
2feb2222077980983eed9271dcb96d74 *R/utils.R
eacbd1a09ba348140a8e37c5b8bcd2e5 *README.md
afdfb96545a980a08b2960eb6d843448 *build/vignette.rds
efd275699c1af73f177feba218748e85 *inst/CITATION
437dd3e137bfdae796424eddcd50cd8b *inst/NEWS
4d9c121a975d33d14ea0e73a7587c3c1 *inst/doc/mapcap_analysis.R
6d7b453e48707b6991a0f3e8da33ae7b *inst/doc/mapcap_analysis.Rmd
0cda7e8379165c533e27bf0c53e7d0da *inst/doc/mapcap_analysis.html
de8b916f9c226200f79c6f55feb85f55 *inst/extdata/bam/embryo1.bam
91e831f3cd3c9f15a9cbc65a5256bdb2 *inst/extdata/bam/embryo1.bam.bai
6f81004281be96947b0a7aec3fd708e9 *inst/extdata/bam/embryo2.bam
d1a7d506ca48f8dfb57fdd27040e8f8f *inst/extdata/bam/embryo2.bam.bai
6f6a1daa30ac3259ea3446b972abcb30 *inst/extdata/bam/embryo3.bam
e9de33af380be5880cfac7aaec779d24 *inst/extdata/bam/embryo3.bam.bai
aec2b788554ef9596a83903bf43de44e *inst/extdata/bam/embryo4.bam
d8936a1cd8f09891df42ecc85f49424a *inst/extdata/bam/embryo4.bam.bai
0c3c740f5e29282a59189275a59021fd *inst/extdata/demult_fastq/embryo1_R1.fastq.gz
bb8a38293ae9c019a76ce993f1acd7ed *inst/extdata/demult_fastq/embryo1_R2.fastq.gz
4b5ba8fca80d6db6eb9a806c1559e828 *inst/extdata/demult_fastq/embryo2_R1.fastq.gz
260725b25ec4e7e437701e2e8f6a6537 *inst/extdata/demult_fastq/embryo2_R2.fastq.gz
d454f40af936e291683c07234337c40b *inst/extdata/demult_fastq/embryo3_R1.fastq.gz
2f4738c18f72cf9bbe1fbe8ac2bf3d2a *inst/extdata/demult_fastq/embryo3_R2.fastq.gz
33836d593cf2d34191e6d9105c28a907 *inst/extdata/demult_fastq/embryo4_R1.fastq.gz
66177ebfbe632de38653de30e626b104 *inst/extdata/demult_fastq/embryo4_R2.fastq.gz
5892afab3371f7e667c4cd3ffa09f4c0 *inst/extdata/filtered_bam/embryo1.filtered.bam
1d08ad34edc7c3dc9969510759247ac8 *inst/extdata/filtered_bam/embryo1.filtered.bam.bai
2cd6075b990efdd8c87fae97df066e06 *inst/extdata/filtered_bam/embryo2.filtered.bam
567e663f982757e1400a5dd3aefd6279 *inst/extdata/filtered_bam/embryo2.filtered.bam.bai
76e22c135d7a09158387e33ca6d1ff9a *inst/extdata/filtered_bam/embryo3.filtered.bam
3648e402b54371182c11737b521615b2 *inst/extdata/filtered_bam/embryo3.filtered.bam.bai
f245afc12a17c7eff49f9d37f803ac72 *inst/extdata/filtered_bam/embryo4.filtered.bam
c417c9d32ffbab6cfb1a11fc6996e409 *inst/extdata/filtered_bam/embryo4.filtered.bam.bai
f9d63ca9f8a24353ec3282ace47b1a41 *inst/extdata/mapcap_test_R1.fastq.gz
c501e7171f176d240536655600de70ed *inst/extdata/mapcap_test_R2.fastq.gz
8d1e334f1e0d86ab90b0a184fb25b1f8 *inst/extdata/testTSS_grl.rds
2d25320c06c1ce89e17f5eac3b14db60 *inst/extdata/testTSS_merged.bed
23e9d05a11b7c5a72d3529382d6d9919 *man/activeChrs.Rd
28981c8578ee00e768f423824f7ce481 *man/annotateTSS.Rd
2888c2e937896b18a256c54f18acc2f1 *man/check_capSet.Rd
108bfe5a9f9cb1f6bd66ea5a8e3970e6 *man/demultiplexFASTQ.Rd
54ad5413b6366a51359f771736a79d92 *man/detectDiffTSS.Rd
e4bfa4fd37519aec20a28c8aeba841f1 *man/detectTSS.Rd
f7da56892af9a90878294afb3fe273cc *man/diffQCplots.Rd
09f1c0b8c40a33d722b77c469f3c4db0 *man/exampleCSobject.Rd
0ac58bcbaae4fbf2440194bf0a3ba3f4 *man/exportTSS.Rd
bfc36e2e2358bb0ba2212b841cc7f97b *man/filterDuplicates.Rd
fa4f50850647daa3d9839c9418536fea *man/filterDups.Rd
043a59b3f083c5ef1c0c495fff6e59a2 *man/fitDiffTSS.Rd
7f129245e2b965269c0c50d5e10fdb4d *man/getBamFlags.Rd
9cb44d1e30a07234078d5578c3d3c7ba *man/getChromBins.Rd
1bce0fb134d399a1b7585e657ba561c0 *man/getChromWindows.Rd
5c30af93b52ab92b2dfb1af94d4a03fb *man/getGeneCounts.Rd
4aef8e3ff4a495897d7c230567b6a94d *man/getMCparams.Rd
33e3807fbb4bd7513e9f34a6740b5179 *man/getNormFactors.Rd
188cc83e2fed34d665d72e7347389013 *man/get_newfastq.Rd
3e4699fc4a2fffd391fa7170aa5062ea *man/getranks.Rd
5392b46b8f4a9274ac1fcefd8226b000 *man/mapCaps.Rd
df7fc4113734fd01af73fd72c9a2031d *man/newCapSet.Rd
91903543bf1ee3eb42ebd20ea584c1a8 *man/numReadsInBed.Rd
8bf2ee8bc854f203ec718c902faf5fb5 *man/plotPrecision.Rd
728c4c4f572951a506ed8fb4e678bd2d *man/plotReadStats.Rd
80e02ccdfc8c6849a9ab66a393e017e4 *man/plotTSSprecision.Rd
0c02304cddaba7f6b8f3cf2682b959d2 *man/readsTo3p.Rd
9c491ebeafafc606d5a7bc6ec688a990 *man/readsTo5p.Rd
26627d0d54336aafe08c654118af025b *man/readsToCenter.Rd
0008f7f192561f790527b2ae4d91d637 *man/sampleInfo.Rd
ff7e5adac8a121a30d611c48a253faea *man/splitBAM_byIndex.Rd
e3e7e8bddf339d25d2fef1b07f431b1c *man/splitBAM_byRepindex.Rd
5214bbb988b5dab4e0756890306b92af *man/split_fastq.Rd
590e4a6319c027697568f7e1b1f83d1b *man/splitranks.Rd
11066325b7455f90d2fb2d3b19284a9b *man/strandBinCounts.Rd
61bf951aa178d1ace27c47dbebb1a70d *tests/testthat.R
4fc6423c0adaca487c25568c21d417cb *tests/testthat/test_CapSet.R
9f13f5d9fd07311f543ba4b20aed0cf0 *tests/testthat/test_annotateTSS.R
929c064f673fb97c7899f05525a4cd96 *tests/testthat/test_demult.R
2f55bb1dae6d69fd9523c260868f398e *tests/testthat/test_filterDups.R
01c64340e1eaa2a2da74a6eae36cc078 *tests/testthat/test_tssDetect.R
6d7b453e48707b6991a0f3e8da33ae7b *vignettes/mapcap_analysis.Rmd
5349479d48e956c791a3cbf24fc5a7a5 *vignettes/references.bib
