bc3b52abf136e20b0149999afc337f4e *DESCRIPTION
67262988fde0cfff764df4ccf857c884 *NAMESPACE
e96382dfc876ba6af180a79ed52adbda *NEWS
d5ee0a88c2ecbc39128e4d3e789978c9 *R/RcppExports.R
bf70513564d8952a6b7a190be1a41391 *R/crosses.R
26eb53f75787d5c81f1aa352b963bc5c *R/dataproc.R
7466268d60a9c6ed13fa0f9e19ca9978 *R/datatools.R
72061eb9659ec0b721a87c5f8e31a175 *R/diversity.R
0988123ae30afe8c10aeda24fbe53a78 *R/docdata.R
a186e0ffef28efdc7076680391c58c2d *R/filters.R
18d7cf76bf4e751aefadf8a6f64e3347 *R/graph.R
18d779083054a272f663d525dad32d09 *R/infoanalysis.R
36c9fe5103b6fbf28de7272b4f113c74 *R/io.R
8a38b40da44b04299acceb1507117a35 *R/kmers.R
ef81c66aa4f2c28c94dd9b4dd0b0bb7c *R/measures.R
f29f5cddfe3ab5afebd426d69233010f *R/mitcr.R
2e63b6f0972f8d0431f28487f1bddc81 *R/onload.R
003ddf6d201f3e1cadd53bb71f8c3ca2 *R/parsing.R
4342989bb5ea7e315739151672da1e26 *R/plots.R
08af695f10104cf351686127c1893def *R/repdiversity.R
2cbafde8bd34f89777ef0658e113207c *R/repoverlap.R
edfd9270866b8578a6d85e371c5874d9 *R/segments.R
37d37da14e85bb2f35e2975d397db13c *R/shared.R
0abf024069438d5e1acc615284782a44 *R/spectrum.R
385c4c5a70bb2b36eb2df94e89bd02c2 *R/stats.R
3257c9831e8d13fbe1d9773f3bddd5ed *R/strtools.R
8168ae00d93f10e79e97ea344da03860 *README.md
96606310b774d068c3bf7a1fa5c77ee2 *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
71c9862006c8c4830ae45e2cfad8459d *inst/doc/tcrvignette.R
6b5ddc9d7590c7c0e16b88f16d6c722c *inst/doc/tcrvignette.Rmd
714dd18d3a7d142722b98887b61d8c50 *inst/doc/tcrvignette.html
0d8030aaef0685c2f34fc53cce1adfac *inst/library.report.Rmd
c435bdc2bef11becfb39297473965a6f *man/AA_TABLE.Rd
90a723ba4e3f02626c45b15f01575c79 *man/apply.symm.Rd
5238a0694a0b87afc116cbb2a4612fcf *man/assymetry.Rd
4a75153ef1837fc632bb89c0d380a23e *man/barcodes.to.reads.Rd
1c4e2d94a67cb971879ff3cc9e957e86 *man/beta.prob.Rd
ddb4199aa5fb662ec8b4acd1ad861ef9 *man/bootstrap.tcr.Rd
9cdcde0cea8c593d9008116bccecad49 *man/check.distribution.Rd
4f72abaed15f5d84cf3bc8d082ff3c97 *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
5b0fd2d2eefac9e721b50ba01031390a *man/convergence.index.Rd
5cf534c8f4b8345056b288334f156e5a *man/cosine.sharing.Rd
cae33fe63680da872daf510c39e56440 *man/cosine.similarity.Rd
fe13a6e7fe9c0ddb8da70d2f4a0d04d6 *man/dot-add.legend.Rd
45a9fd13d13c843fb5f1a2cf77fe72af *man/dot-column.choice.Rd
1adff722e109f9c7b1920c1fcce11f53 *man/dot-fix.listnames.Rd
7268c9769743640c41e0de7aad697c80 *man/dot-verbose.msg.Rd
c317ef8bd85fbbceb5e7f0b673e804e0 *man/entropy.Rd
ba90872f88c7f11218828fd806c44877 *man/entropy.seg.Rd
42eb3b21c6f698c0490294a86af35daf *man/find.clonotypes.Rd
f24fcd3b87d5d1af3f9b24fb989836bd *man/find.similar.sequences.Rd
e1dac959fd2d6125725835399f96ba38 *man/fix.alleles.Rd
69c32ef27966d5b68855d74b7d059890 *man/gc.content.Rd
5ecfd113b6aa8af4a75894f394e45594 *man/geneUsage.Rd
a41e2b66d4d58ebc706f06ad9ea38e82 *man/generate.kmers.Rd
fa670137405d50fbf4e10af9be30bcb9 *man/generate.tcr.Rd
77d869dd81f03a18c9b13f4cc6f60718 *man/get.all.substrings.Rd
d050e0d04851896b80848db375d12497 *man/get.deletions.alpha.Rd
75d3126f6c18a8aefb8244d314b342f3 *man/get.inframes.Rd
752bae53e58fd8db0bbd89a59a5ca8a8 *man/get.kmers.Rd
8bf4a3e542a5fbc70c1eade55ad3b3af *man/gibbs.sampler.Rd
80ed39ff37aa19524e6c26f72b3bf2db *man/group.clonotypes.Rd
224edc9f1d69178168b9ab1f96c45a59 *man/has.class.Rd
2d2d486f075d7c509e48f238aa6ad400 *man/intersectClonesets.Rd
c9622086734076b437c6edfe091a185b *man/inverse.simpson.Rd
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7275fa10b7a105901d44d68d3d115f49 *man/kmer.table.Rd
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24bd4592bb2206ac57b98904c46f3069 *man/matrixSubgroups.Rd
15f4bc51a432da7c7f470bfe5b4a190d *man/matrixdiagcopy.Rd
80dced59953149a95fb739289228db28 *man/mutated.neighbours.Rd
8fae995180d68ed5d7bd949005a22882 *man/mutation.network.Rd
21a2fd34b0dfaa7c562f87eb95103253 *man/ozScore.Rd
57d3e854e2be1397e328abb4e1d7413d *man/parse.cloneset.Rd
b2d955a325dbd67be5ed0fa4735fe6a5 *man/parse.folder.Rd
60ffe7cab7d8d53ab3c20b551423c1c2 *man/pca.segments.Rd
4b86d56ff3d5dd0823580cc8fafe1c93 *man/pca2euclid.Rd
aa1d8777719192402e4492adef44811c *man/permutDistTest.Rd
3008fa41aebb5bb4f66cb29d9ff2faeb *man/permutedf.Rd
507fb9e5d3cddd4a7b442adbbd5b788e *man/rarefaction.Rd
7be0d6a29b4f9a96c0ded480a591817c *man/repDiversity.Rd
9a4fbea17c030f054c736203b6e8068e *man/repLoad.Rd
c21c460980d8f7152855938c3390c675 *man/repOverlap.Rd
a9de808bd49dddf8f992d838b04c40b7 *man/repSave.Rd
80d9930f1b2beb81e03b095c187dafc5 *man/resample.Rd
e81568d029b718a8d6feddb5b765d9c0 *man/revcomp.Rd
adeceae0833a6c459ab6749a9f10fdee *man/reverse.string.Rd
e46c4ee7e2c4181135b64f183619aa24 *man/sample.clones.Rd
8954424a5a7ecff72c01ba52a102b4d5 *man/sample2D.Rd
810e07ead9e26541f0ebceaf740bd6e9 *man/segments.alphabets.Rd
d6efddff8f2903791b7df1a37147ec67 *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
156279a726fd1a47d1adc5b0bc312498 *man/spectratype.Rd
475d3feda165f1a631cedc3edb0d0ea0 *man/startmitcr.Rd
74a61db9271c466bd24ccdfdda3bedec *man/tailbound.proportion.Rd
698e3e45ff0bf8a7398686c9bc8c0913 *man/top.cross.Rd
1782facd22b9ac8771fcd07c87482d86 *man/top.fun.Rd
6d12f87c7b96bfb095a526970e901154 *man/twinsdata.Rd
876ed3d1f6c6eae70f286a33fe54a6ef *man/vis.clonal.dynamics.Rd
7554171f87709835f7ca77c15be6501e *man/vis.clonal.space.Rd
d7c0f006c4601622f70b577b300f82e0 *man/vis.count.len.Rd
55cfc879425f317692ff748958fcf57d *man/vis.gene.usage.Rd
5512bb5426b0717eb5ed84b006cace68 *man/vis.group.boxplot.Rd
dbd71235f03ca2046bae03483ee778ea *man/vis.heatmap.Rd
28dcac8cb544c9d99d629af1a66cde01 *man/vis.kmer.histogram.Rd
f7e68343dba989624d96ab04921db617 *man/vis.logo.Rd
e140ddca96c69a7b792072a77b7e9ad5 *man/vis.number.count.Rd
2eafe6f2544ac207a33fa289ab8bac53 *man/vis.pca.Rd
48d0d03c171f07c8ac9bd0a80bd13a69 *man/vis.radarlike.Rd
a400389cae7e4d0ae2e2ff2770e96649 *man/vis.rarefaction.Rd
59367ba73ee78bd4270671180c1110f2 *man/vis.shared.clonotypes.Rd
60ab1c6d69a2e78b8edbb1b12e743e2f *man/vis.top.proportions.Rd
e3d3cb360fbfdb3c6974e14eb5f09870 *src/Makevars
2460e6e93c37da9409c7b4c1959a28a4 *src/RcppExports.cpp
8613b0d97d73171a1f6a526d93a87ee9 *src/neighbour.search.cpp
6b5ddc9d7590c7c0e16b88f16d6c722c *vignettes/tcrvignette.Rmd
