342032127b0933898ef7720780724afc *DESCRIPTION
cabcc026b607c650d29bbaed664be1ee *NAMESPACE
bee9a4cd22111b6de46ed4cd38b662f2 *NEWS.md
bd59d21a7fb7b938b99a0ffcc7e24914 *R/Alakazam.R
0c7e1e6726bb43b768906db6540b2341 *R/AminoAcids.R
f6e0d1fce17fe087df552218004a6be9 *R/Classes.R
6425a23855eeea913faa8855a5ebbcc0 *R/Core.R
362b28b0a5ead69128c5d0e5e59664fd *R/Data.R
86e564b8b709c13ca72e80296a455980 *R/Deprecated.R
1f8aedcd8b4aa759cafccf9efd7b340a *R/Diversity.R
c9bdee2a3a5e4916aef326268fb16468 *R/Fastq.R
8a21659f0c0f879d65b57123b91b51a2 *R/Gene.R
49cad9f838747121c9b2d1cf82bf6ace *R/Lineage.R
6f8a72642969fd382cd8f88bc18e6b24 *R/RcppExports.R
36f781a6b4b261508aba59a7bda57abb *R/Sequence.R
0727444d4b16f44f29bb4461adfa4e50 *R/Topology.R
def92a4fe63ca7bcdba22c3a382dbced *R/sysdata.rda
16abe98bf5ac519c0a8ffd6c3bae3a18 *README.md
ad8c7b82e60df06a48ecf74ddfab640e *build/vignette.rds
8e55f0c4422bff63d5f9a73636ccd2ea *data/Example10x.rda
00d346df4989b70e5ae4029101c56941 *data/ExampleDb.rda
44a2714d7443c83b5cf8d6f7b21c252e *data/ExampleDbChangeo.rda
e21a9d5c5dd3aeae144c615b41f70133 *data/ExampleTrees.rda
b034dfc6972e3bdd19b8801d55ac4b7e *inst/CITATION
19c6dfc4ea2e7e338178015f02cf5fea *inst/doc/AminoAcids-Vignette.R
960653fdeb23924745066c49cd80e31a *inst/doc/AminoAcids-Vignette.Rmd
c0a0f14f4ac5e162fa60f50d14ef980d *inst/doc/AminoAcids-Vignette.pdf
700fa8bdfc792634f2b5873186104d0f *inst/doc/Diversity-Vignette.R
8d6d91b988a00e8a70a86c4047bd9ffc *inst/doc/Diversity-Vignette.Rmd
2672ee60f770a91f885c593dbbdf5073 *inst/doc/Diversity-Vignette.pdf
dfd8ae51f5168ada4a2842f6b3ed4ea2 *inst/doc/Fastq-Vignette.R
d38d32e47bdc65cb35e328a02640c968 *inst/doc/Fastq-Vignette.Rmd
a5d9849daae3aab81984fa270ad8ed92 *inst/doc/Fastq-Vignette.pdf
9d129fbe25a9f2be19b083e23549d621 *inst/doc/Files-Vignette.R
e83df6ce6b04a14b1eedfc8cf85935b4 *inst/doc/Files-Vignette.Rmd
736ec51a80807f10ad2a820229305a6c *inst/doc/Files-Vignette.pdf
316b9e92df2066a0f3f72ec7d8bb1022 *inst/doc/GeneUsage-Vignette.R
802b6f439b64a29cf7dacffb426aa24a *inst/doc/GeneUsage-Vignette.Rmd
17c4ead1981bd00de81257b59e53c2fc *inst/doc/GeneUsage-Vignette.pdf
9a06e7ab9acf7316d267a736ea0624f1 *inst/doc/Lineage-Vignette.R
af66b5b13a8679da7628b4440b8657d4 *inst/doc/Lineage-Vignette.Rmd
902255714674f47cee4e6c9939998cce *inst/doc/Lineage-Vignette.pdf
e20fababa3ab7cde6ffcc92b8b2b3ee5 *inst/doc/Topology-Vignette.R
666709ad33269e1852458f8bd1b51735 *inst/doc/Topology-Vignette.Rmd
0f92d5c3b33b36fd63e6a04c870ae23d *inst/doc/Topology-Vignette.pdf
d6b9c5b466e6acfac01f41f70279e462 *inst/extdata/example_airr.tsv.gz
2fcc671e7657eed4ee9b6819004d9563 *inst/extdata/example_changeo.tab.gz
547e6794bb28cdeb9d355bea001d77ba *inst/extdata/example_quality.fastq
a859f8de5695231a17a684df638aff58 *inst/extdata/example_quality.tsv
987475fe1f56c385e720c6afd798dd08 *man/ABBREV_AA.Rd
12bc2f6e5c83021ba446013f93f2c819 *man/AbundanceCurve-class.Rd
13bf964a5e2d342c91185034bf2bb2cb *man/ChangeoClone-class.Rd
a84a6d4edd8410275bb1abd5a463ad32 *man/DEFAULT_COLORS.Rd
e8cf58a2dee521487a4c4c64af7a793f *man/DiversityCurve-class.Rd
ddc49fed05c59121028f0dabecbe5fb1 *man/EdgeTest-class.Rd
1932908e3468566f4df4b03b421a5948 *man/Example10x.Rd
407424a705d79f858d4e57db2caab842 *man/ExampleDb.Rd
40db6c9c2338f5fee3bc9d1c8c9ce4e9 *man/ExampleDbChangeo.Rd
6e69b6b8867ec8ce3d7a0df5da568603 *man/ExampleTrees.Rd
8715b738946f7c22ce18b077e0f8b724 *man/IMGT_REGIONS.Rd
4585817f760a903f7ad773fff25573f5 *man/IUPAC_CODES.Rd
4d8441622f8bbb14de45524ceecbe737 *man/MRCATest-class.Rd
2ff2d4ad04c36645af1cb93497b1df21 *man/alakazam.Rd
db19819685d940da24bd3022a9d4e8be *man/aliphatic.Rd
14d7a80970ef09bd37bda31b80e04b1d *man/alphaDiversity.Rd
9c6358d65ad5b0b301e9f1959f6d6f68 *man/aminoAcidProperties.Rd
a8d03c199086e18e26fd673624ffa1a4 *man/baseTheme.Rd
dee250ff18cd924dfcb0f019a6388201 *man/buildPhylipLineage.Rd
bbfdb6340b92a396e2b4bb5f15cd5633 *man/bulk.Rd
c686bdeedc7abc3277241668dfe4bb2f *man/calcCoverage.Rd
af307d6e0209dbd3acaf15c8ec4c8295 *man/calcDiversity.Rd
f5d0c57b59e2dc17cc82c1d59e29d4dd *man/charge.Rd
995aabe2f257ba72862d5b226ce03c66 *man/checkColumns.Rd
7c682c648b3a05217b526850f09d1b42 *man/collapseDuplicates.Rd
c3719294a76cb1dc606b0115b935be90 *man/combineIgphyml.Rd
e40fd4846b4eeb3836e10b9bae834506 *man/countClones.Rd
ad2f576a3db27d486cd17d1d4f617fe9 *man/countGenes.Rd
f18bcc0f36fc2bad4d104181caa77fb0 *man/countPatterns.Rd
228c0d1d4a6fc2744f10623b6342ead8 *man/cpuCount.Rd
2a319c89da2b5e3d33054136acfa3d91 *man/estimateAbundance.Rd
9dd006c3a64d4b51deafeecdbb805fac *man/extractVRegion.Rd
d9bcf6fa4885d0682e7f951faf7f2254 *man/getAAMatrix.Rd
f3d1c78e3419a6d133ac41d1b340edb6 *man/getDNAMatrix.Rd
da9177951218d3a90104d18255531f86 *man/getMRCA.Rd
d97054f355e98a82cf5a5a806526ed5b *man/getPathLengths.Rd
18e41b200a453d4a5b9a28b0babdb50a *man/getPositionQuality.Rd
82a6342458d201f139b8266bb117d4ab *man/getSegment.Rd
76697bcf036a02fbe6ddb7f351926ca9 *man/graphToPhylo.Rd
ebd8bf4d329181cffdec5346ad8721ee *man/gravy.Rd
43a957cfa4f3285543fad47363376786 *man/gridPlot.Rd
86a06adb5a779690a2d79547d8a24802 *man/groupGenes.Rd
56bbb424640d95b6e9fcb109c76df6f5 *man/isValidAASeq.Rd
06c223e80ce92f32f5a2c495b9d8a6e3 *man/makeChangeoClone.Rd
16c622dc1a843365e20d348978727214 *man/makeTempDir.Rd
d977ffb1591f5c93f326241acd133275 *man/maskPositionsByQuality.Rd
1eeab523917cc47d245c324644f4a387 *man/maskSeqEnds.Rd
18ef28997eb2cb4a67ae7f06c4856f6d *man/maskSeqGaps.Rd
c4ee04b0eacd1e93066cc87c0520800d *man/nonsquareDist.Rd
7ff01dba7bb52b0f78b5fe6e8883faab *man/padSeqEnds.Rd
1e23c90638621a4425fc49ced382dc0c *man/pairwiseDist.Rd
a93f7fde10257f4d80ca1a3db58ebcaf *man/pairwiseEqual.Rd
f0e407fd33a9a29bf63240fefb36c724 *man/permuteLabels.Rd
c380b34307cbbee5f99ba5e2b06f4efc *man/phyloToGraph.Rd
1464ab02cdbdde56bf43bf2fb09896c0 *man/plotAbundanceCurve.Rd
3a398759982862f3c309f41f5d93f204 *man/plotDiversityCurve.Rd
5b9a7c245bdc2ce91dad0b34777140c1 *man/plotDiversityTest.Rd
b04ce7ad42cc547cad4f6d868ff121b8 *man/plotEdgeTest.Rd
a5b7b7857f7d7af28283f046db9d47ce *man/plotMRCATest.Rd
a2f316fb3a25fb9d7264a991800d13d8 *man/plotSubtrees.Rd
57f38289101ef92fa9db938e09766869 *man/polar.Rd
7c2c3846d5f429596501499da0c9aec9 *man/progressBar.Rd
6649627271c10d1be5d87687c649e762 *man/rarefyDiversity.Rd
749b4b8b9daca586ea634d209ecbaf74 *man/readChangeoDb.Rd
ded74283da2084401944c9ed4e06ae4a *man/readFastqDb.Rd
a580831b84edd79a88f34cc693d3e597 *man/readIgphyml.Rd
7cc1917257918b65d8ff2c5e0f47e93c *man/seqDist.Rd
f5e27a7fa978350281f109893235c4d4 *man/seqEqual.Rd
1e0a5d095b881bde9dfa4603903b23e5 *man/sortGenes.Rd
4551455c0ab7d85eba44ccab82ddccd5 *man/stoufferMeta.Rd
a70b6eafc7cbb3753f60afe631379f3e *man/summarizeSubtrees.Rd
68a832553b26782673d82eeaedea750c *man/tableEdges.Rd
3308f5dd254a011be415178f8b17b710 *man/testDiversity.Rd
30c9e033d03b8ae1362aa6bb31de7aa7 *man/testEdges.Rd
20882770192a22a72305d094fbd60a70 *man/testMRCA.Rd
ed2b5d2d9fd87a693a560dd5fd7fdf7f *man/translateDNA.Rd
8242a3df101301f23473a572115fc432 *man/translateStrings.Rd
0fae9e0a11ec04f6fc43723538408b95 *man/writeChangeoDb.Rd
3b377cf40c356ccde3fa098907bfd279 *src/RcppDistance.cpp
abf7eb815358ba8bbf07451999ce055e *src/RcppExports.cpp
960653fdeb23924745066c49cd80e31a *vignettes/AminoAcids-Vignette.Rmd
8d6d91b988a00e8a70a86c4047bd9ffc *vignettes/Diversity-Vignette.Rmd
d38d32e47bdc65cb35e328a02640c968 *vignettes/Fastq-Vignette.Rmd
e83df6ce6b04a14b1eedfc8cf85935b4 *vignettes/Files-Vignette.Rmd
7a6f6601aa4fbcbb6cee349e7dfe5587 *vignettes/Files-Vignette.html
802b6f439b64a29cf7dacffb426aa24a *vignettes/GeneUsage-Vignette.Rmd
af66b5b13a8679da7628b4440b8657d4 *vignettes/Lineage-Vignette.Rmd
666709ad33269e1852458f8bd1b51735 *vignettes/Topology-Vignette.Rmd
