674458df9271cedab6128140173d0218 *DESCRIPTION
ed6485eda4a1889ffac224192bf9f07b *NAMESPACE
f80aab859d09e45330ae6f35480f68ec *NEWS.md
32b61fa932efa50c8fda8bb71a3efd6d *R/Alakazam.R
ac3d757b655945c9c26fe584a6ec7118 *R/AminoAcids.R
f81ef9176e96a80bb2bfc6a12422cf70 *R/Classes.R
0807b912b9127e5971ebf5bb78b41110 *R/Core.R
71edf30ff926aa0f3c09394df9ca1e93 *R/Data.R
4fac75c94c5dc66c1503ffc25212265d *R/Deprecated.R
6614d8a3f24c6a8680ba649565672c58 *R/Diversity.R
c9bdee2a3a5e4916aef326268fb16468 *R/Fastq.R
ac1a3bac1f989f8384630acf4144362d *R/Gene.R
a8e1528509b247ae8c00d7ac9dfc69dc *R/Lineage.R
6f8a72642969fd382cd8f88bc18e6b24 *R/RcppExports.R
43da19eddf0ad470ea60274a87ad421c *R/Sequence.R
e4cb54c098026cdf296d0aff6599a4f7 *R/Topology.R
def92a4fe63ca7bcdba22c3a382dbced *R/sysdata.rda
0ce0f2c7ea401d834b25edb6234ecdbf *README.md
af3401175684b1e7ff4b3d3b8941c6eb *build/partial.rdb
cd488a967cc6b683bf96424eb04f138c *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
2d39c897c084dd8694a79307011b3b11 *inst/doc/AminoAcids-Vignette.pdf
93ba4b12ce025f154eefba075a0ad8e6 *inst/doc/Diversity-Vignette.R
a2c89a9cf48062d46104d77e8f9f474f *inst/doc/Diversity-Vignette.Rmd
7082811bca019b66ddef4060fb8ef340 *inst/doc/Diversity-Vignette.pdf
ddd0dc0980ee355a5114b98ff2a97ce8 *inst/doc/Fastq-Vignette.R
bc1ee42a0d0f5be791bd1f6d7e9eaca7 *inst/doc/Fastq-Vignette.Rmd
c78f82021cfedc4e4541d1fdfdfda490 *inst/doc/Fastq-Vignette.pdf
1d2e0d9136c6d75a95564ebc0c38a6b5 *inst/doc/Files-Vignette.R
e83df6ce6b04a14b1eedfc8cf85935b4 *inst/doc/Files-Vignette.Rmd
8a8118e3a5d70b60e36d69b3b3b58b19 *inst/doc/Files-Vignette.pdf
35e9193b29e6087483cdca358c2c9a4f *inst/doc/GeneUsage-Vignette.R
e3ee207abe0ce9261ffa223e788fcc5d *inst/doc/GeneUsage-Vignette.Rmd
dcd1d4d9e74f62c51459b83d53595e40 *inst/doc/GeneUsage-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
9984cb333b62eb6d54df5188899f5d4a *man/AbundanceCurve-class.Rd
1865f875fe65a4f90246a68446fd9399 *man/ChangeoClone-class.Rd
a84a6d4edd8410275bb1abd5a463ad32 *man/DEFAULT_COLORS.Rd
fe18069131a614b6f119ab12bbd4f870 *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
c9edbdf0ebda5e884732d53be2eabd62 *man/MRCATest-class.Rd
3b369061d3f5a02afc617e3bdcdc6f74 *man/SingleDb.Rd
dc4c6860390e58ffc85bc22d0bf30182 *man/alakazam-package.Rd
1fe888fc83446431a5c83bb141724566 *man/alakazam.Rd
db19819685d940da24bd3022a9d4e8be *man/aliphatic.Rd
14d7a80970ef09bd37bda31b80e04b1d *man/alphaDiversity.Rd
ac7db0bbbb451f89d065020acf2943a6 *man/aminoAcidProperties.Rd
a8d03c199086e18e26fd673624ffa1a4 *man/baseTheme.Rd
2188fa4b91cde905b65da90ce7b1c50c *man/buildPhylipLineage.Rd
bbfdb6340b92a396e2b4bb5f15cd5633 *man/bulk.Rd
c686bdeedc7abc3277241668dfe4bb2f *man/calcCoverage.Rd
af307d6e0209dbd3acaf15c8ec4c8295 *man/calcDiversity.Rd
42c99ea962c520a3d6cb6b88572ad984 *man/charge.Rd
995aabe2f257ba72862d5b226ce03c66 *man/checkColumns.Rd
4e8068f197386ef3186f0e4f4c407f78 *man/collapseDuplicates.Rd
1edcf4295bdcc9d9ae06d7bf3b89caa5 *man/combineIgphyml.Rd
37681bc65c9671b7cbbd4772bb252935 *man/countClones.Rd
6bc4ce3781edef19b33d14923fbecde3 *man/countGenes.Rd
e53becee13b70f2005243881ad2cb6e4 *man/countPatterns.Rd
228c0d1d4a6fc2744f10623b6342ead8 *man/cpuCount.Rd
cbb3d8fda724bb4236422c52f9e4f942 *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
898317ea6c420342bd7145c831893611 *man/getSegment.Rd
76697bcf036a02fbe6ddb7f351926ca9 *man/graphToPhylo.Rd
ebd8bf4d329181cffdec5346ad8721ee *man/gravy.Rd
d76480d11876bffe3d8724fbec516b6e *man/gridPlot.Rd
fa596f64f9942f59fd3a00cf2c74452e *man/groupGenes.Rd
56bbb424640d95b6e9fcb109c76df6f5 *man/isValidAASeq.Rd
a9acf8807ef75725f015d91f0869fd64 *man/junctionAlignment.Rd
89f037a76206f4ae41689f2277d07207 *man/makeChangeoClone.Rd
16c622dc1a843365e20d348978727214 *man/makeTempDir.Rd
d977ffb1591f5c93f326241acd133275 *man/maskPositionsByQuality.Rd
1eeab523917cc47d245c324644f4a387 *man/maskSeqEnds.Rd
18ef28997eb2cb4a67ae7f06c4856f6d *man/maskSeqGaps.Rd
1dbeea7d8ca4d987e66eec4298e34f15 *man/nonsquareDist.Rd
7ff01dba7bb52b0f78b5fe6e8883faab *man/padSeqEnds.Rd
1e23c90638621a4425fc49ced382dc0c *man/pairwiseDist.Rd
a93f7fde10257f4d80ca1a3db58ebcaf *man/pairwiseEqual.Rd
f0e407fd33a9a29bf63240fefb36c724 *man/permuteLabels.Rd
c380b34307cbbee5f99ba5e2b06f4efc *man/phyloToGraph.Rd
a2ccc1960f51fa22cc5868297967ec86 *man/plotAbundanceCurve.Rd
eaaa2a39adadc8fcf35b10d416d48cb2 *man/plotDiversityCurve.Rd
202d728968c9933121d825d175e49dce *man/plotDiversityTest.Rd
af5d9096d8470f1f895d4bc07ad2d0fc *man/plotEdgeTest.Rd
553a53b5b0a96f390422a565fee9d970 *man/plotMRCATest.Rd
14f6a8cb7dbdf6658e827dabb856ea65 *man/plotSubtrees.Rd
57f38289101ef92fa9db938e09766869 *man/polar.Rd
7c2c3846d5f429596501499da0c9aec9 *man/progressBar.Rd
0db2c1713974b92925667f80f1a7862d *man/rarefyDiversity.Rd
a07a1db2516b5e3389f7632e93ce8fab *man/readChangeoDb.Rd
ded74283da2084401944c9ed4e06ae4a *man/readFastqDb.Rd
cf495c29c7882c26a3ae89454ac7ab78 *man/readIgphyml.Rd
7cc1917257918b65d8ff2c5e0f47e93c *man/seqDist.Rd
f5e27a7fa978350281f109893235c4d4 *man/seqEqual.Rd
0c647e5454dc4290d946b9fb409e9723 *man/sortGenes.Rd
4551455c0ab7d85eba44ccab82ddccd5 *man/stoufferMeta.Rd
a70b6eafc7cbb3753f60afe631379f3e *man/summarizeSubtrees.Rd
68a832553b26782673d82eeaedea750c *man/tableEdges.Rd
b40be779af7ec82fb400f257504f2070 *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
a2c89a9cf48062d46104d77e8f9f474f *vignettes/Diversity-Vignette.Rmd
bc1ee42a0d0f5be791bd1f6d7e9eaca7 *vignettes/Fastq-Vignette.Rmd
e83df6ce6b04a14b1eedfc8cf85935b4 *vignettes/Files-Vignette.Rmd
e3ee207abe0ce9261ffa223e788fcc5d *vignettes/GeneUsage-Vignette.Rmd
