637a22fc99e5acb59767b2cdb9b63e8f *DESCRIPTION
ed6485eda4a1889ffac224192bf9f07b *NAMESPACE
b6f26a592609e1a93941cdf97130c033 *NEWS.md
38f343a432567a39846afb0dd908e7d2 *R/Alakazam.R
d71ea375dbdcb26f8276cd99093cfe80 *R/AminoAcids.R
f6e0d1fce17fe087df552218004a6be9 *R/Classes.R
916ace3ad514cd4a531390016089db24 *R/Core.R
71edf30ff926aa0f3c09394df9ca1e93 *R/Data.R
86e564b8b709c13ca72e80296a455980 *R/Deprecated.R
86e4518b872982ed1d5dc644774525e9 *R/Diversity.R
c9bdee2a3a5e4916aef326268fb16468 *R/Fastq.R
0ff86e7bd3b6e597a36624e9606ed351 *R/Gene.R
0dfe0f1ef0cb6c1a90077f16d875b118 *R/Lineage.R
6f8a72642969fd382cd8f88bc18e6b24 *R/RcppExports.R
8db48271b2b0f99470c9b4ad71524273 *R/Sequence.R
c8581d9d8bef8d6ab416568664e22bd3 *R/Topology.R
def92a4fe63ca7bcdba22c3a382dbced *R/sysdata.rda
3398ce3684e5d65869b119635bbf1b51 *README.md
7080893e02c49cd296d4424b9be55069 *build/partial.rdb
31ad388c6c5e035944abc19531fedeee *build/vignette.rds
8e55f0c4422bff63d5f9a73636ccd2ea *data/Example10x.rda
2ca0c64c8ed79f363f7b06e171839818 *data/ExampleDb.rda
44a2714d7443c83b5cf8d6f7b21c252e *data/ExampleDbChangeo.rda
9456c9ccc04b81b1acdaa564afbbf243 *data/ExampleTrees.rda
26bc36d9477eb80794992f0aab49f5c0 *data/SingleDb.rda
b034dfc6972e3bdd19b8801d55ac4b7e *inst/CITATION
d9d5ababa8ef62395f5398046b516a97 *inst/doc/AminoAcids-Vignette.R
960653fdeb23924745066c49cd80e31a *inst/doc/AminoAcids-Vignette.Rmd
a5687f6a3dfe98bade32201905e77253 *inst/doc/AminoAcids-Vignette.pdf
b5dda44fd2ba0f1235f5eb7fa50382ce *inst/doc/Diversity-Vignette.R
b43702f2123e679b9ded2ff921037eb1 *inst/doc/Diversity-Vignette.Rmd
1924bfe7c14457ba2f109363143926c2 *inst/doc/Diversity-Vignette.pdf
ddd0dc0980ee355a5114b98ff2a97ce8 *inst/doc/Fastq-Vignette.R
bc1ee42a0d0f5be791bd1f6d7e9eaca7 *inst/doc/Fastq-Vignette.Rmd
f02f3a445eaf362e74f0645a60683724 *inst/doc/Fastq-Vignette.pdf
0d56c8162b4e38ac04cbb3b322dd6d15 *inst/doc/Files-Vignette.R
e83df6ce6b04a14b1eedfc8cf85935b4 *inst/doc/Files-Vignette.Rmd
c562a8e8bd62db483d08cfb295d98534 *inst/doc/Files-Vignette.pdf
651b31226485ec0c7f6180296aab17a8 *inst/doc/GeneUsage-Vignette.R
802b6f439b64a29cf7dacffb426aa24a *inst/doc/GeneUsage-Vignette.Rmd
4d969e19e904456fb221d77fae3ea39a *inst/doc/GeneUsage-Vignette.pdf
a9af24d2533d799ac06566e7ffb260b8 *inst/doc/Lineage-Vignette.R
8a9e73918c83119ac0ce6e1710c46185 *inst/doc/Lineage-Vignette.Rmd
3133cc18d3ead10cd6bd7da373be31f2 *inst/doc/Lineage-Vignette.pdf
d75c1f36f70c370f5dae8775763671c3 *inst/doc/Topology-Vignette.R
e7e008c78c5c17e3e46edefbb6508230 *inst/doc/Topology-Vignette.Rmd
b937176450bbef0ae5145d5b9c42144e *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
6853dbdd976e24e406dcc39c824f277e *man/IMGT_REGIONS.Rd
4585817f760a903f7ad773fff25573f5 *man/IUPAC_CODES.Rd
4d8441622f8bbb14de45524ceecbe737 *man/MRCATest-class.Rd
3b369061d3f5a02afc617e3bdcdc6f74 *man/SingleDb.Rd
81eebe9b035eb3a5cb769688944abe68 *man/alakazam-package.Rd
2e74f2c7fe2ef4fe67a22877ac25be0a *man/alakazam.Rd
db19819685d940da24bd3022a9d4e8be *man/aliphatic.Rd
14d7a80970ef09bd37bda31b80e04b1d *man/alphaDiversity.Rd
d7b2caf979401d440a9648ef7ee00159 *man/aminoAcidProperties.Rd
a8d03c199086e18e26fd673624ffa1a4 *man/baseTheme.Rd
1182a86ad7f76f2574fea18001f8c752 *man/buildPhylipLineage.Rd
bbfdb6340b92a396e2b4bb5f15cd5633 *man/bulk.Rd
c686bdeedc7abc3277241668dfe4bb2f *man/calcCoverage.Rd
af307d6e0209dbd3acaf15c8ec4c8295 *man/calcDiversity.Rd
42c99ea962c520a3d6cb6b88572ad984 *man/charge.Rd
995aabe2f257ba72862d5b226ce03c66 *man/checkColumns.Rd
7c682c648b3a05217b526850f09d1b42 *man/collapseDuplicates.Rd
c3719294a76cb1dc606b0115b935be90 *man/combineIgphyml.Rd
e40fd4846b4eeb3836e10b9bae834506 *man/countClones.Rd
ad2f576a3db27d486cd17d1d4f617fe9 *man/countGenes.Rd
e53becee13b70f2005243881ad2cb6e4 *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
ccc0565b7266c496c29802830241f448 *man/getSegment.Rd
76697bcf036a02fbe6ddb7f351926ca9 *man/graphToPhylo.Rd
ebd8bf4d329181cffdec5346ad8721ee *man/gravy.Rd
43a957cfa4f3285543fad47363376786 *man/gridPlot.Rd
86a06adb5a779690a2d79547d8a24802 *man/groupGenes.Rd
56bbb424640d95b6e9fcb109c76df6f5 *man/isValidAASeq.Rd
a9acf8807ef75725f015d91f0869fd64 *man/junctionAlignment.Rd
30de8901dfdc3e828c32d115941e010f *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
dddb082d641c0c2e74d542fc33ad960c *man/plotAbundanceCurve.Rd
36271c575b7282997a2c552c1a1ce830 *man/plotDiversityCurve.Rd
5b9a7c245bdc2ce91dad0b34777140c1 *man/plotDiversityTest.Rd
af5d9096d8470f1f895d4bc07ad2d0fc *man/plotEdgeTest.Rd
553a53b5b0a96f390422a565fee9d970 *man/plotMRCATest.Rd
14f6a8cb7dbdf6658e827dabb856ea65 *man/plotSubtrees.Rd
57f38289101ef92fa9db938e09766869 *man/polar.Rd
7c2c3846d5f429596501499da0c9aec9 *man/progressBar.Rd
6649627271c10d1be5d87687c649e762 *man/rarefyDiversity.Rd
a07a1db2516b5e3389f7632e93ce8fab *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
2dc1fded59f2f258192ddb2d9b9a72c5 *man/testEdges.Rd
6afbc7577d809e0fef8278d5060a9c9d *man/testMRCA.Rd
ed2b5d2d9fd87a693a560dd5fd7fdf7f *man/translateDNA.Rd
8242a3df101301f23473a572115fc432 *man/translateStrings.Rd
04cb7509996ed099f47415db4fec4e03 *man/writeChangeoDb.Rd
3b377cf40c356ccde3fa098907bfd279 *src/RcppDistance.cpp
48e120890b196a5e995ea895e4f926be *src/RcppExports.cpp
960653fdeb23924745066c49cd80e31a *vignettes/AminoAcids-Vignette.Rmd
b43702f2123e679b9ded2ff921037eb1 *vignettes/Diversity-Vignette.Rmd
bc1ee42a0d0f5be791bd1f6d7e9eaca7 *vignettes/Fastq-Vignette.Rmd
e83df6ce6b04a14b1eedfc8cf85935b4 *vignettes/Files-Vignette.Rmd
802b6f439b64a29cf7dacffb426aa24a *vignettes/GeneUsage-Vignette.Rmd
8a9e73918c83119ac0ce6e1710c46185 *vignettes/Lineage-Vignette.Rmd
e7e008c78c5c17e3e46edefbb6508230 *vignettes/Topology-Vignette.Rmd
