684458daadca9b6ff16a40d1d9ccfadc *DESCRIPTION
29a9012941a6bcb26bf0fb4382c5dd75 *LICENSE
c58b208970d7f899b2307c5dab889fc5 *NAMESPACE
5326b525559cdcc19905e6008fcccf3f *R/CTSSs.R
334dea6167f52a9e9b257bb7f51881dd *R/aaa.R
6d3443c497e8aea8146e06e62d941b63 *R/assign.R
56f3f67bfdf747d7c073508972accb72 *R/bam.R
680cd9ed35623c6463df546abb6344c5 *R/bw.R
3dfaf4605f464f6d2b5ddbc870f9c678 *R/calc.R
df530012f414450516a219da51857cfb *R/check.R
2a9680fa16de20020bbe98bd136feeb8 *R/cluster.R
30ca338c74513fed5ba47a74053dde7f *R/combine.R
f3f481176075c22dea34a8eb1c6bc610 *R/convert.R
6305d85a260dd34fd6569a78358a39cb *R/enhancers.R
eec1feb624d67008dbd598f4e655f6e1 *R/example.R
4de929de2a93af3809b92601c499e700 *R/find.R
2b05f5c596de6497cb041768752d7753 *R/quantify.R
ee707deeb52f909c83c2341c9fa6937b *R/quick.R
0d8bf89a7107d650897a067f1849f241 *R/rowsum2.R
ff13e29489537336c704518e92274d1f *R/shape.R
37a4042c72afd7e28f9a15069f15c010 *R/split.R
70e5f00ba089e462db770173b24f4ae9 *R/subsetBy.R
c4ffcb54ca177ae4c7b236a337bdb416 *R/swap.R
0d5eea61ffdef7960db7144174f72077 *R/track.R
62690ae2e2363b654fe13ec3db7f8817 *R/trimTo.R
d7cd3394c28ec9cd3aec687ee843786c *R/tune.R
f253ce06945abe3f6ba6b898415cc725 *R/utils.R
f1a079db4cfde5e1dab4c6c995adf63a *R/zzz.R
27bcff776bf9f65f554a51eb4fb4c359 *README.md
dda68eec3daa83ed49f0320f7adba94b *build/vignette.rds
26d213518f47d0c9d2c3b59490b42935 *data/exampleBidirectional.rda
43a8d05c5c735b223ad6db107a65a4f2 *data/exampleCTSSs.rda
1595ea74223fd6d8100a6a13f8bd76b1 *data/exampleDesign.rda
ff829851df8e6a9810301aef0845a18c *data/exampleGenes.rda
b45ca05cd5be54269c1c214dd5fd03e3 *data/exampleUnidirectional.rda
90f2fd9569ff1ab9a9e85c771e0dce40 *inst/CITATION
3aadbb010cdca8636bc58b6b8fe266c3 *inst/NEWS
8ae1e7ab4b70d10348e929e9ec4a2b9b *inst/doc/Introduction_to_CAGEfightR.R
9728419f0f7d7181bbce11d5ba46ba89 *inst/doc/Introduction_to_CAGEfightR.Rmd
77a0e77ba56ed6c68dfeb61dae88e09b *inst/doc/Introduction_to_CAGEfightR.html
d1addb1b161c5d2d029a54dbf03aba45 *inst/extdata/mm9.C547.minus.bw
12abbe7c0e853f44d353c3f819055f32 *inst/extdata/mm9.C547.plus.bw
4c3a45077f5ecf6e93427c4800a0085d *inst/extdata/mm9.C548.minus.bw
56befdc837745f8b2a5811e3ea94f8b0 *inst/extdata/mm9.C548.plus.bw
246381ce67e76f4f772af9406fddd109 *inst/extdata/mm9.C549.minus.bw
ac58aa74ba527e06166c70747ab63537 *inst/extdata/mm9.C549.plus.bw
9f06bfc0404f89311cc4f426fbb6cf2a *man/assignGeneID.Rd
80e1377acef8a08fc20362eb2301bb09 *man/assignMissingID.Rd
1e73177dd1efc87a4fa752a4bd1a3039 *man/assignTxID.Rd
c9487e6630195db6430505358312c01f *man/assignTxType.Rd
e2a9760c92c4f3f4d38af0adb8242332 *man/balanceBC.Rd
81750eaf05acb35cd3910313b1ed5bf5 *man/balanceD.Rd
5dc744a8bc0a70d36b373c7fb0e945c3 *man/bwCommonGenome.Rd
c47d8cdf9744541bf8e51adc8b84ae5b *man/bwGenomeCompatibility.Rd
f6aad8c853eb5436ce083020f5215eff *man/bwValid.Rd
756513842ce53a73b44c447f2f0dc198 *man/calcBidirectionality.Rd
ff280e32100c5a6737a1b1affb7c6f97 *man/calcComposition.Rd
c8e9cef5c0d67d23a0789a48f8d2852a *man/calcPooled.Rd
94cf658c2489d78de971688bf14d6d74 *man/calcShape.Rd
05857d88237a07d152a7111940806361 *man/calcSupport.Rd
968cb7c23885bfc5c960c9fe116a4d27 *man/calcTPM.Rd
4969e7816026f76cb08d4be33554d713 *man/calcTotalTags.Rd
91543d85f33d9b39eb4537f63834f3f2 *man/checkCTSSs.Rd
0c3771776c33de8153f0a9f93835c56d *man/checkPeaked.Rd
591fc7c0b8e5010cf063ca2d024816e3 *man/checkPooled.Rd
6266014b7dfa7d7e97feb8f4bf27639e *man/clusterBidirectionally.Rd
65128a6718c138baea1370cf768b71af *man/clusterUnidirectionally.Rd
0f95091af159a671a541d73a0b7cb1c5 *man/combineClusters.Rd
0d0cc2fe0355c30fc39395883f328a80 *man/convertBAM2BigWig.Rd
cc69fab2a44819b2d63f2c967f1eb4c0 *man/convertBED2BigWig.Rd
448b12727e42324a20553d23d96501d7 *man/convertGRanges2GPos.Rd
6689a0060d97410de7c1a9f24078fc8c *man/exampleDesign.Rd
d05c900fa882ba96f490f249b4af2931 *man/findLinks.Rd
f00ef3c23f22143cb808543e352f34ef *man/findStretches.Rd
6801240e1f031ab3ae15a0db20b29dd9 *man/quantifyCTSSs.Rd
07050f045bd16cbe387a304f4b5dc085 *man/quantifyCTSSs2.Rd
80d347c5754c7383aec66d380a43b7a6 *man/quantifyClusters.Rd
3a835e4a408c34e0fd8f7c3c0885e60d *man/quantifyGenes.Rd
67b308ebab37fa081869f11a312f01eb *man/quickEnhancers.Rd
1daff565bf92dad8b7faf9c70fa4cf8c *man/quickGenes.Rd
671c9702982fe1c9f03a77e803af7301 *man/quickTSSs.Rd
fef8ee37dfccf23d4e602552ed1ada82 *man/shapeEntropy.Rd
09769fcd01a890b4058fcbd4ad7ef393 *man/shapeIQR.Rd
cde3c5f8005fb05c35ee611365078323 *man/shapeMean.Rd
0dc3f77506226bd92ee80e277cbf503a *man/shapeMultimodality.Rd
60b3b8f5d360213dc3d1e3728a25a713 *man/subsetByBidirectionality.Rd
1a6ea9b1dd3aa20a9bb9e78dd53a97da *man/subsetByComposition.Rd
0f8cd36dcd8a861083c6b0eaa8081ae5 *man/subsetBySupport.Rd
28862e9eaeb00254fc1a28825908b76f *man/swapRanges.Rd
d03dc2afb44a4df1bc740597fa21ad62 *man/swapScores.Rd
6a7fbc9bc1167410308f62686b386744 *man/trackBalance.Rd
0985e3fd0957e191ae1173b0599edcef *man/trackCTSS.Rd
ad6eae441e537fee9d1e962c3f7e07b5 *man/trackClusters.Rd
8b661a57d402ccc0dffd1910ef6bfcd6 *man/trackLinks.Rd
ba875d4e349d0253363cff9e0ddfb9a3 *man/trimToPeak.Rd
e746ce2207d8a79230f1f846021a7185 *man/trimToPercentiles.Rd
8a1aacec1fdcdb804438d30329bc463b *man/tuneTagClustering.Rd
99f79fcc61599087e2209aebdce97605 *man/utilsAggregateRows.Rd
334e858ede963db89e639124157fc91f *man/utilsDeStrand.Rd
59b22342c9dcbc13de47bbfcd9df16dc *man/utilsScoreOverlaps.Rd
33d120a77ba17452140c0c94fdde7b8d *man/utilsSimplifyTxDb.Rd
9728419f0f7d7181bbce11d5ba46ba89 *vignettes/Introduction_to_CAGEfightR.Rmd
