022e8065637690c53d8eb69fdd94604f *DESCRIPTION
03344dfc32e4d40eb0c1111876f14b0e *NAMESPACE
e96382dfc876ba6af180a79ed52adbda *NEWS
d5ee0a88c2ecbc39128e4d3e789978c9 *R/RcppExports.R
bf70513564d8952a6b7a190be1a41391 *R/crosses.R
26eb53f75787d5c81f1aa352b963bc5c *R/dataproc.R
d52da366e68bd598acf5041d250f83a1 *R/datatools.R
72061eb9659ec0b721a87c5f8e31a175 *R/diversity.R
0988123ae30afe8c10aeda24fbe53a78 *R/docdata.R
a186e0ffef28efdc7076680391c58c2d *R/filters.R
18d7cf76bf4e751aefadf8a6f64e3347 *R/graph.R
18d779083054a272f663d525dad32d09 *R/infoanalysis.R
b5681159c5404b92e7a8147952691346 *R/io.R
59d4ebee4bc11f561168740429bf3597 *R/kmers.R
ef81c66aa4f2c28c94dd9b4dd0b0bb7c *R/measures.R
f29f5cddfe3ab5afebd426d69233010f *R/mitcr.R
c08854821f7b0b223e4db194602d4055 *R/onload.R
003ddf6d201f3e1cadd53bb71f8c3ca2 *R/parsing.R
4342989bb5ea7e315739151672da1e26 *R/plots.R
feb13c7a0cc1c669359c5130eeb37d9b *R/repdiversity.R
635731a172dec20b18715fc60f8b00b9 *R/repoverlap.R
2a02d33cb664073101c0fd99ca4a7da8 *R/segments.R
0bac2b82ac075c676934af5dc34de7a8 *R/shared.R
0abf024069438d5e1acc615284782a44 *R/spectrum.R
385c4c5a70bb2b36eb2df94e89bd02c2 *R/stats.R
3257c9831e8d13fbe1d9773f3bddd5ed *R/strtools.R
ba8ca92d871c1406e7d409edc91546c9 *README.md
90a53f30e4b9e9e7f045de8c2232de76 *build/vignette.rds
89d6d3f555bed92c5ed36af98b04c7a4 *data/beta.prob.rda
0b472b1afd448af9612974a7033a82bb *data/datalist
3e5199fd3d3acb248adfe09b59f39bfd *data/genesegments.rda
802f976ee11eb67c9d8f3be6669004f2 *data/twa.rda
8253da4f56f8eee73ad14945e15ab374 *data/twb.rda
9beb0651b51d566bb9ba008ae0bf49ac *inst/CITATION
32815f3b1b3683089c10c05523e2a13c *inst/crossanalysis.report.Rmd
b3e30dfc5fa127c08986ec4efbf74f9b *inst/doc/tcrvignette.R
eeab2cf8838689cf2aa096201ac32813 *inst/doc/tcrvignette.Rmd
595c0f280553d64b2145f904ce0c0d6e *inst/doc/tcrvignette.html
0d8030aaef0685c2f34fc53cce1adfac *inst/library.report.Rmd
4deaa0317a24a10bc6d8320f3377eb53 *man/AA_TABLE.Rd
90a723ba4e3f02626c45b15f01575c79 *man/apply.symm.Rd
5238a0694a0b87afc116cbb2a4612fcf *man/assymetry.Rd
4a75153ef1837fc632bb89c0d380a23e *man/barcodes.to.reads.Rd
6af0e87235e6e4d2850015811ad087b3 *man/beta.prob.Rd
69f49c950172b8133278e5a21dc8ecb0 *man/bootstrap.tcr.Rd
5e11c8a90beac719baaaa1e7347caced *man/check.distribution.Rd
8d6f96d407ca50f08110da1bf569ea10 *man/clonal.space.homeostasis.Rd
b7bfe4dcfc9ad8ff6beb0c832fe3a05c *man/cloneset.stats.Rd
cb2a04e9548ca95b0bd6c4182add8d96 *man/codon.variants.Rd
c58ea39a436a784b22264c3a994e775f *man/column.summary.Rd
eda87e8c588a04b5db3aa951a161da73 *man/contamination.stats.Rd
0a0086484f862c962785f4f9d964e6cb *man/convergence.index.Rd
1f45c6b9d5a511da337786701bb22505 *man/cosine.sharing.Rd
cae33fe63680da872daf510c39e56440 *man/cosine.similarity.Rd
c317ef8bd85fbbceb5e7f0b673e804e0 *man/entropy.Rd
ba90872f88c7f11218828fd806c44877 *man/entropy.seg.Rd
48013374daccbd07437f67de6b79657e *man/find.clonotypes.Rd
f24fcd3b87d5d1af3f9b24fb989836bd *man/find.similar.sequences.Rd
e1dac959fd2d6125725835399f96ba38 *man/fix.alleles.Rd
69c32ef27966d5b68855d74b7d059890 *man/gc.content.Rd
235dc8f8014be65c8cf21304bb80ff50 *man/geneUsage.Rd
a41e2b66d4d58ebc706f06ad9ea38e82 *man/generate.kmers.Rd
88a387ff84e45ea0f9ec0957b38d416c *man/generate.tcr.Rd
77d869dd81f03a18c9b13f4cc6f60718 *man/get.all.substrings.Rd
d050e0d04851896b80848db375d12497 *man/get.deletions.alpha.Rd
75d3126f6c18a8aefb8244d314b342f3 *man/get.inframes.Rd
825c286de186b655962edeb5a9a788bd *man/get.kmers.Rd
8bf4a3e542a5fbc70c1eade55ad3b3af *man/gibbs.sampler.Rd
8bdedc09585b94c4f3ee0ff24299c650 *man/group.clonotypes.Rd
224edc9f1d69178168b9ab1f96c45a59 *man/has.class.Rd
2d2d486f075d7c509e48f238aa6ad400 *man/intersectClonesets.Rd
c9622086734076b437c6edfe091a185b *man/inverse.simpson.Rd
b61fdb16f4f0008069b9ec243bef86b1 *man/kmer.profile.Rd
7275fa10b7a105901d44d68d3d115f49 *man/kmer.table.Rd
b5096e2299c2a9bfd42a7f502d51b783 *man/loglikelihood.Rd
24bd4592bb2206ac57b98904c46f3069 *man/matrixSubgroups.Rd
15f4bc51a432da7c7f470bfe5b4a190d *man/matrixdiagcopy.Rd
80dced59953149a95fb739289228db28 *man/mutated.neighbours.Rd
7a5dd2f97fd1ad58dd92dcd236fa51a3 *man/mutation.network.Rd
b2372947d044951eaa107e785531ac82 *man/ozScore.Rd
4eb4aca54aa3cbbdf443a898bf3b6a37 *man/parse.cloneset.Rd
b2d955a325dbd67be5ed0fa4735fe6a5 *man/parse.folder.Rd
60ffe7cab7d8d53ab3c20b551423c1c2 *man/pca.segments.Rd
4b86d56ff3d5dd0823580cc8fafe1c93 *man/pca2euclid.Rd
530a1ebfdab540bc476e857724e8512a *man/permutDistTest.Rd
3008fa41aebb5bb4f66cb29d9ff2faeb *man/permutedf.Rd
47f783f10b21707944b1827e4e9106a3 *man/rarefaction.Rd
dff2a6ebd6f6f2544b9b92c02780d425 *man/repDiversity.Rd
9a4fbea17c030f054c736203b6e8068e *man/repLoad.Rd
8b6217e008858aa5727c0b38d572efcb *man/repOverlap.Rd
a9de808bd49dddf8f992d838b04c40b7 *man/repSave.Rd
80d9930f1b2beb81e03b095c187dafc5 *man/resample.Rd
87b54475ed26e7ef1e2cb3eb33dc6fc5 *man/revcomp.Rd
adeceae0833a6c459ab6749a9f10fdee *man/reverse.string.Rd
e46c4ee7e2c4181135b64f183619aa24 *man/sample.clones.Rd
8954424a5a7ecff72c01ba52a102b4d5 *man/sample2D.Rd
d9d64a89ec690618bd4f9ab2c7e18272 *man/segments.alphabets.Rd
d54b1ae3158552bdd63e3c69aa2cb666 *man/segments.list.Rd
c01802b5e78f0654615f046cace2d83a *man/set.group.vector.Rd
3f3ba65839cc9cdb90dbf8b09da7abc8 *man/set.pb.Rd
6845de0d4ddd068621ed7e8f5a969b65 *man/set.people.vector.Rd
92d9582d8cd9dc7141f5d8f637024f53 *man/set.rank.Rd
43aff234930d14d353a773e88b1da72f *man/shared.repertoire.Rd
8dee47c9755bb501664427d238bcba52 *man/spectratype.Rd
a9dd971fea010fd34acfe8727407e0aa *man/startmitcr.Rd
74a61db9271c466bd24ccdfdda3bedec *man/tailbound.proportion.Rd
698e3e45ff0bf8a7398686c9bc8c0913 *man/top.cross.Rd
7cd750dd1025165164ba653566097045 *man/top.fun.Rd
c386e872be02c894e7f939c86631ccc3 *man/twinsdata.Rd
876ed3d1f6c6eae70f286a33fe54a6ef *man/vis.clonal.dynamics.Rd
7554171f87709835f7ca77c15be6501e *man/vis.clonal.space.Rd
d7c0f006c4601622f70b577b300f82e0 *man/vis.count.len.Rd
cba42e7ebea224bb52a2943b40a7090f *man/vis.gene.usage.Rd
8c38b330ac3a378fb68d4142100e067e *man/vis.group.boxplot.Rd
32b676112a3aeefbc5a4eaefc8107d3e *man/vis.heatmap.Rd
b9db5a59919d5da270d64e210b5cce26 *man/vis.kmer.histogram.Rd
6ee61a06fff7d50b7d073dc1a7a66953 *man/vis.logo.Rd
c7e8e68901d2cc971c8b30b12b8ee685 *man/vis.number.count.Rd
2eafe6f2544ac207a33fa289ab8bac53 *man/vis.pca.Rd
48d0d03c171f07c8ac9bd0a80bd13a69 *man/vis.radarlike.Rd
a400389cae7e4d0ae2e2ff2770e96649 *man/vis.rarefaction.Rd
36a00a3421fa4508ffc85226596415d9 *man/vis.shared.clonotypes.Rd
fd46db8c9948fcfaeff32c4e4267f805 *man/vis.top.proportions.Rd
e3d3cb360fbfdb3c6974e14eb5f09870 *src/Makevars
2460e6e93c37da9409c7b4c1959a28a4 *src/RcppExports.cpp
8613b0d97d73171a1f6a526d93a87ee9 *src/neighbour.search.cpp
eeab2cf8838689cf2aa096201ac32813 *vignettes/tcrvignette.Rmd
