648d8320661ee7db1768f8ac6503b368 *DESCRIPTION
94826a47b450fd7173a92beb72664dc3 *NAMESPACE
a492484c01e95e6d4723ad31b10e671f *R/RcppExports.R
a691a4a56cbdbf8af72c8e80f6c681fa *R/crosses.R
9a9c8e37d09c047af3c4e5e9c8027d0c *R/dataproc.R
43e05a6c40058c300c87c5d0f6d14455 *R/datatools.R
906616fc95b3bfe767deb05b25522f74 *R/diversity.R
7ce2551187d261afb61679269dceafc3 *R/docdata.R
aa15a1051bb4e38152fbdb906b938bdc *R/filters.R
8d235fad5ece2fcf3e44cd9785d34901 *R/infoanalysis.R
953bc3aca08cbc15da6a5604f19d5558 *R/input.R
8d2d2f79a0a428beb0f794082db3cf34 *R/kmers.R
dc023da35b61de7cfba4b1b0fa9d5b27 *R/measures.R
f29f5cddfe3ab5afebd426d69233010f *R/mitcr.R
3a34ef0a567c7b76cfafc6e7226659fa *R/plots.R
de42b2dd0a0dd48435447c054d48767f *R/segments.R
618e6d5d0de1201ab92462f0693bc058 *R/shared.R
19f5791187fee653b336b878b11ff013 *R/spectrum.R
89bf13c5d3b511a27458adcf3317149d *R/stats.R
774c3b5e525ef0dd44aab4dc2a334d17 *R/strtools.R
6ac671a983590c51afba951a6e1fa69b *README.md
c54e5946c38fe3ed005235f8b9e9da1c *build/vignette.rds
89d6d3f555bed92c5ed36af98b04c7a4 *data/beta.prob.rda
4d9440071c98aae99e2ab606b6937b98 *data/datalist
e8b5fa68587985dfcabed1d11fb69a9f *data/human.alphabets.rda
abb4660e8bfebc115ad4f237589f1567 *data/mouse.alphabets.rda
cf2088a88997923cc775d50024f53b88 *data/segments.rda
c2b8052c95095af33344e99139b56106 *data/twa.rda
de9bc89e695e977f4f3bcbf7c70dbc8d *data/twb.rda
64738eb1939ce8d5e468cb42468db0f9 *inst/CITATION
9d91442b41ce56e71e01266500a95838 *inst/crossanalysis.report.Rmd
9796c3a21b2e4efef4697dcb050dd14c *inst/doc/tcrvignette.R
fd695ffd8e2c84003f88089ea7083aad *inst/doc/tcrvignette.Rnw
d7e698e5ce5c6f04a026eb82bed46f60 *inst/doc/tcrvignette.pdf
e26ef75e50ef9a525d1c9b0dd80b000a *inst/library.report.Rmd
caeb9b830859ee4ad8bde23868f64cfc *man/AA_TABLE.Rd
8dd6192d6fa2eb7e767bec5963cae369 *man/apply.symm.Rd
03170f098cf0edf18dd86e9d7313135c *man/assymetry.Rd
cdc56b933b8be8bf0f429e3d7a09906d *man/barcodes.to.reads.Rd
fcc5c41e7fa89fa4819aa908161dac99 *man/beta.prob.Rd
bf4ddad3d0e766dc035ccec6402c6fae *man/bootstrap.tcr.Rd
5cba9f13f0cd3aed3281e793a35182f9 *man/check.distribution.Rd
2c21efc67d3c2ba58796fe17f9da7a65 *man/codon.variants.Rd
2bf390b342dd5603efc1cc24f15dafba *man/column.summary.Rd
9cd97cc0f7d3db5cec6e792eae2186fb *man/contamination.stats.Rd
b91a72f3fb88b39b5dccbba2ad637d49 *man/convergence.index.Rd
e059772098066ac91ae9b6674fb709ef *man/cosine.sharing.Rd
da77fe25940ac5845b20d8ddff93fb28 *man/cosine.similarity.Rd
3537e5f1f8e3ecd6d8ff2417e3eaab4d *man/entropy.Rd
2301c90f001ebcd75504cd9baef0dcd7 *man/entropy.seg.Rd
8372dd5bc9cc5bae2071ddcbd7c1440b *man/find.clonotypes.Rd
63135bcd402fa57eeb9e00491c4ea4be *man/find.similar.sequences.Rd
377733476c7435f78519ebe34670a9ec *man/freq.segments.Rd
6cebec1c0994bfed09c871f77e196517 *man/gc.content.Rd
224aa22254e674c8d49bc8d4d3994878 *man/generate.kmers.Rd
5eca32c3b698ae4d37e6ba8e2154ffec *man/generate.tcr.Rd
4ff8562a739cdc9b30875d9938904dbd *man/get.all.substrings.Rd
88cf99945b63e1537fbedf40bfce6d32 *man/get.deletions.alpha.Rd
64b27d76ddffc1f1f19f8ee3db52839e *man/get.inframes.Rd
c168a951be812edca6b01579cde5202c *man/get.kmers.Rd
1ff80b0d52738e1b8874ced343d123cc *man/get.n.barcodes.Rd
76e3daeb2df549ab3f402526788387a1 *man/gibbs.sampler.Rd
3d0c24f6239ed7578fb468e7dcc2c62c *man/has.class.Rd
ac46a947e6d2cc1b6961a3a5b2e967bb *man/intersect.Rd
e8fad867b6871fd504f695aa9530905e *man/inverse.simpson.Rd
86e95829754ebc08a8339ca33caacdf8 *man/kmer.profile.Rd
8fb13ee0c4b77d5988bea55aa2f3c02b *man/kmer.table.Rd
e6bea42ba6d591ca5bdde0ea4195fbf8 *man/loglikelihood.Rd
1e59fdddef717cbbca526f4de71be4ba *man/matrixdiagcopy.Rd
6a16974ce8de79514d740f53ef695114 *man/mitcr.stats.Rd
81eaa440fe3b40b4e49b1f3e69c5f1c9 *man/parse.file.Rd
385f5c0c84cab1c8507ebd2f695ff61a *man/parse.file.list.Rd
502d5605aed522ce1484b93f9ca30c27 *man/parse.folder.Rd
fd7719694f855e805168093a5228cdd3 *man/pca.segments.Rd
7cad0835e6a3941ccdd67943bb504ec8 *man/permutedf.Rd
258f265b237e77dd04b31c0635c57c34 *man/rarefaction.Rd
546acecf909b5015a99ce48e61c1003b *man/revcomp.Rd
d936a900f21191a29ab0ca01a36cb030 *man/reverse.string.Rd
a233e1b331bc0c471596673e5d60c1fe *man/sample.clones.Rd
5630efe09a42e385f24347b12e18772c *man/sample2D.Rd
9699c06ce67be2cf96a2f6a08e68b251 *man/segments.alphabets.Rd
b2b31846cb828c8a5811f7e67a7f07e3 *man/segments.list.Rd
7c87f9d1d9615f0300a91e12d3410598 *man/set.pb.Rd
835dca82fc55a92b70b8effc8765a253 *man/set.rank.Rd
2ad4ba270a74813a5b0d5292470ddfc5 *man/shared.repertoire.Rd
a03073802a66597cc352b61995886531 *man/spectratyping.Rd
922d8494e71fc4f7930806b986742d72 *man/startmitcr.Rd
0907bb8b54df388743f575be32888145 *man/tailbound.proportion.Rd
1982c81cc67f14b61888f4d65c9e0bff *man/top.cross.Rd
b23191dd3bac9ab95c457a889c065530 *man/top.fun.Rd
cbf7d61751f652cdcccc46ae9fad9038 *man/twinsdata.Rd
dcc94cd1fff790438fbf91cd88d8a4fb *man/vis.V.usage.Rd
a2b2151e2a71637528045d59f712c1fa *man/vis.clonal.dynamics.Rd
ba018c1acb22e05bf297a10355ac03de *man/vis.count.len.Rd
85dd18b50dce0c6bcebceeb964a6373f *man/vis.group.boxplot.Rd
54c88ebf9dcea11750499708a3d6eec7 *man/vis.heatmap.Rd
9deecb22b558e42ae4da5acc94fdcdf0 *man/vis.kmer.histogram.Rd
55613f1897ef0de4dc1f865197c4fb70 *man/vis.number.count.Rd
213fa41d70b0500f122b82a5c3f0ac6c *man/vis.pca.Rd
c2d4db25c023aad9c8378d5b50e94bf5 *man/vis.radarlike.Rd
317ecc55964fbf5cf8b0142a957475d8 *man/vis.rarefaction.Rd
36d59bf5bb8603f1e5fbf9619b84e860 *man/vis.top.proportions.Rd
e3d3cb360fbfdb3c6974e14eb5f09870 *src/Makevars
7bd7f519490a8efc01f17def91bdb310 *src/RcppExports.cpp
8a553b2fb838c974dd86da98b4d6264c *src/neighbour.search.cpp
fd695ffd8e2c84003f88089ea7083aad *vignettes/tcrvignette.Rnw
