5c7ea904d4e68f12ecc410a80e9a0fee *DESCRIPTION
81b40fe5f80f38453166e1003170d20e *NAMESPACE
9861b8a4ccb2156daf2570cda0cb127f *NEWS.md
764913dfe4a49c93563560c432e31bd7 *R/Alakazam.R
144056e211e941b8ae15184b2adbeb08 *R/AminoAcids.R
f81ef9176e96a80bb2bfc6a12422cf70 *R/Classes.R
74f909df72bc66c7d7ec703a9aa373a9 *R/Core.R
71edf30ff926aa0f3c09394df9ca1e93 *R/Data.R
4fac75c94c5dc66c1503ffc25212265d *R/Deprecated.R
748a4ca3684cd317c8d6ee4e56e8f05c *R/Diversity.R
bc417e54be26f75cc97d6aceb2436953 *R/Fastq.R
1f05ba40a9748f1b26c779f6f92333f2 *R/Gene.R
dd4847e2b35f9eb84c9df45666039583 *R/Lineage.R
c037e0938fdd7027ea47f002cac24773 *R/RcppExports.R
9d4d86296735b593169675c756ba5dbe *R/Sequence.R
a7a555cbfae9379046eaaeb3df422a76 *R/Topology.R
def92a4fe63ca7bcdba22c3a382dbced *R/sysdata.rda
4d0c2b3d6a1fc57dbe58b2a678fd22c6 *README.md
c5260b1bae00ec1fb8d54bd1b69b28ba *build/partial.rdb
d66ef5e24458fe3f34a0a8e1c8128f7c *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
1e445632d6742bfb157a783657d1ad56 *inst/doc/AminoAcids-Vignette.Rmd
ca365cc89e54f2a1bf59b7a1067b8949 *inst/doc/AminoAcids-Vignette.pdf
8f066387595894f05ee183f67f222725 *inst/doc/Diversity-Vignette.R
ba830d78923a7a12b13f23f9a0e71448 *inst/doc/Diversity-Vignette.Rmd
855948a1c868724e2670e2eb77ab6d1a *inst/doc/Diversity-Vignette.pdf
cf667fd9690f5a4fdcd5b07ff30c22c0 *inst/doc/Fastq-Vignette.R
199dce42660e42db6459be8b6e62d83f *inst/doc/Fastq-Vignette.Rmd
7d942510e415df8f8ab4eed7aa3b3ffb *inst/doc/Fastq-Vignette.pdf
1d2e0d9136c6d75a95564ebc0c38a6b5 *inst/doc/Files-Vignette.R
e83df6ce6b04a14b1eedfc8cf85935b4 *inst/doc/Files-Vignette.Rmd
03b33a923329abf4fed60032c78e09ed *inst/doc/Files-Vignette.pdf
35e9193b29e6087483cdca358c2c9a4f *inst/doc/GeneUsage-Vignette.R
e3ee207abe0ce9261ffa223e788fcc5d *inst/doc/GeneUsage-Vignette.Rmd
36da68eb747fcd6ffbc9643a2990390f *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
f6be4841138a5beda0925768be8f9ec2 *man/ABBREV_AA.Rd
9984cb333b62eb6d54df5188899f5d4a *man/AbundanceCurve-class.Rd
1865f875fe65a4f90246a68446fd9399 *man/ChangeoClone-class.Rd
cf8a6716bd96e542dd04e12a96f031c4 *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
db9ba35885aeccd3884c2899c1ddbbb2 *man/IMGT_REGIONS.Rd
35d6ec254cd72635744378640c359e6c *man/IUPAC_CODES.Rd
c9edbdf0ebda5e884732d53be2eabd62 *man/MRCATest-class.Rd
3b369061d3f5a02afc617e3bdcdc6f74 *man/SingleDb.Rd
2db74c4ccfdb2eed9cee518c73443d60 *man/alakazam-package.Rd
793a7467f7c2f58c3e7fd416268716f4 *man/alakazam.Rd
db19819685d940da24bd3022a9d4e8be *man/aliphatic.Rd
e9e465c8a8a26950241c8c25615f9d65 *man/alphaDiversity.Rd
ac7db0bbbb451f89d065020acf2943a6 *man/aminoAcidProperties.Rd
a8d03c199086e18e26fd673624ffa1a4 *man/baseTheme.Rd
c2f3dd4c4c45130c31c1e6ac3ad012bc *man/buildPhylipLineage.Rd
bbfdb6340b92a396e2b4bb5f15cd5633 *man/bulk.Rd
c686bdeedc7abc3277241668dfe4bb2f *man/calcCoverage.Rd
af307d6e0209dbd3acaf15c8ec4c8295 *man/calcDiversity.Rd
42c99ea962c520a3d6cb6b88572ad984 *man/charge.Rd
995aabe2f257ba72862d5b226ce03c66 *man/checkColumns.Rd
fd32268d61abfdcdf60385ea9cee3653 *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
9a68f557844aafde0b1531fe5e1db0b7 *man/fastDist.Rd
1a27bb7de0182cbb22d34ae994463194 *man/fastDistAA.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
1f220e42363b4ad643d1f07947a95aa7 *man/makeTempDir.Rd
d977ffb1591f5c93f326241acd133275 *man/maskPositionsByQuality.Rd
1eeab523917cc47d245c324644f4a387 *man/maskSeqEnds.Rd
18ef28997eb2cb4a67ae7f06c4856f6d *man/maskSeqGaps.Rd
ff6dcf2db79d6a7e41538c21bf5774a4 *man/nonsquareDist.Rd
7ff01dba7bb52b0f78b5fe6e8883faab *man/padSeqEnds.Rd
1e23c90638621a4425fc49ced382dc0c *man/pairwiseDist.Rd
ab9e14ceb659e113d1e9a57d2ac11c7c *man/pairwiseEqual.Rd
c5f561c5488e65d0c1b0114ace1c06bb *man/permuteLabels.Rd
c380b34307cbbee5f99ba5e2b06f4efc *man/phyloToGraph.Rd
a2ccc1960f51fa22cc5868297967ec86 *man/plotAbundanceCurve.Rd
eaaa2a39adadc8fcf35b10d416d48cb2 *man/plotDiversityCurve.Rd
202d728968c9933121d825d175e49dce *man/plotDiversityTest.Rd
af5d9096d8470f1f895d4bc07ad2d0fc *man/plotEdgeTest.Rd
c2e94bf7c23a6e9b1669aa1e8099ec6b *man/plotMRCATest.Rd
14f6a8cb7dbdf6658e827dabb856ea65 *man/plotSubtrees.Rd
57f38289101ef92fa9db938e09766869 *man/polar.Rd
7c2c3846d5f429596501499da0c9aec9 *man/progressBar.Rd
0db2c1713974b92925667f80f1a7862d *man/rarefyDiversity.Rd
ec0e2cca7c7afa3aaa4693e495e33a5f *man/readChangeoDb.Rd
ded74283da2084401944c9ed4e06ae4a *man/readFastqDb.Rd
cf495c29c7882c26a3ae89454ac7ab78 *man/readIgphyml.Rd
7cc1917257918b65d8ff2c5e0f47e93c *man/seqDist.Rd
f5e27a7fa978350281f109893235c4d4 *man/seqEqual.Rd
e9fc6839d40515c4d9414aa205556bde *man/seqMismatchCount.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
c2e74ad86fed485d8a0874e97127e355 *man/writeChangeoDb.Rd
fe2922f91e545962807635e5c8a25f57 *src/RcppDistance.cpp
ace41b0b8efc25efbbb7846adced433f *src/RcppExports.cpp
13b3a7f9220d118fa55cafcfeb299abe *src/RcppSeqMismatch.cpp
a0c6acfad7b78fdbcaba71c549a67e8b *src/fastDist.cpp
8736a2922767cafe840dba0ee58301dc *src/fastDistAA.cpp
1e445632d6742bfb157a783657d1ad56 *vignettes/AminoAcids-Vignette.Rmd
ba830d78923a7a12b13f23f9a0e71448 *vignettes/Diversity-Vignette.Rmd
199dce42660e42db6459be8b6e62d83f *vignettes/Fastq-Vignette.Rmd
e83df6ce6b04a14b1eedfc8cf85935b4 *vignettes/Files-Vignette.Rmd
e3ee207abe0ce9261ffa223e788fcc5d *vignettes/GeneUsage-Vignette.Rmd
