c5e2628828084bcdde0195bdbd28b137 *DESCRIPTION
86c0b651bfa817b420bdda5df31a7ac4 *NAMESPACE
12c69188cd29de7f9a766fea3799c967 *R/CrisprRun.R
d86b56e5ad5073d6979196184e776d1c *R/CrisprSet.R
c31e219dd5879882087b63bdce70903a *R/abifToFastq.R
234adfc779bcc17792b7531bcf1047d9 *R/accessors.R
6cac3e230335639b6612ad0f68195e8a *R/alleleLabels.R
d54d9e11e18135567ccfdc9d55eaeef1 *R/barplotAlleleFreqs.R
f01aa428f8b4d97abc854c438a050f22 *R/crispRvariants_data.R
13b2925b3d3df6d5edf91f6a02bad690 *R/excludeFromBam.R
6d8d69bf3e67224e00b8a557e12e8087 *R/findChimeras.R
2d154180b98d23418bde71fb5a2926aa *R/getInsertionsTable.R
86724f170f9d16091ff94d482f8ffcbf *R/initialisers.R
b2a674550001371ae22f6edd2321f1cb *R/input_checks.R
166d12fca390b2c9701f1483a430ef0d *R/mergeChimeras.R
9f8f5e3f9bf8305f1d57ed4c92cad9ef *R/narrowAlignments.R
8c56d613a01b2b2e128678fc30f4950f *R/plotAlignments.R
950b294a99d079408fa0f92b9b8af748 *R/plotChimeras.R
0eb3aeffd6909a647508967ea825b7e7 *R/plotFreqHeatmap.R
f87e46a822de7c0410348d1e2375d873 *R/plotVariants.R
febc42ce3c3bb5dd40fb800691984186 *R/readsByPCRPrimer.R
a97dbe4bf38830955a15c4c2fba1adf0 *R/refFromAlns.R
ffb5e9e6a7aef2047e20fc3531438ad1 *R/reverseCigar.R
210c9129d6c6fb233ecee01a7a2eb29f *R/seqsToAln.R
03962efdaa862d3a1358c6ba613a597c *R/utils.R
fde284727b48f3441d2e9d0cc82e80d7 *R/writeFastq.R
725eaee84abc3fda60bbc85bc7115d73 *build/vignette.rds
e56808e76f5a0ae49923700efb4acc3f *data/gol_clutch1.rda
4ad19164b71f48a159aee0245eee9ad2 *inst/CITATION
590504cacc0084a282f24e3746aedeb4 *inst/NEWS.Rd
8e7ea48597bb1f1af03e9829d62e7ed5 *inst/doc/user_guide.R
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450c2953ea85c135325e0f18b08d1623 *inst/doc/user_guide.pdf
65dcdf1d72c2cb6532b582faf9648242 *inst/extdata/Danio_rerio.Zv9.73.gol.sqlite
3d09e19e1a84f4163a94c7ac41b4d7a1 *inst/extdata/GRCz10_81_ptena_txdb.sqlite
cb32a40b50b777c9872e74844182b9cc *inst/extdata/IM2033.ab1
31f41ba5b5f3ffe65a72638ac48d59ee *inst/extdata/ab1/ptena/phenotype/embryo1/AB2001.ab1
87fbf13a52e1801266cb385c7919a4e9 *inst/extdata/bam/ab1_ptena_phenotype_embryo_1_s.bam
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aa172362f53fb84dfc85ff43e8b58232 *inst/extdata/bam/ab1_ptena_phenotype_embryo_2_s.bam
64f942fe93f6cb37549443b020be66bd *inst/extdata/bam/ab1_ptena_phenotype_embryo_2_s.bam.bai
dbfe81d150812e6f46063d6e3af8a7e9 *inst/extdata/bam/ab1_ptena_uninjected_embryo_1_s.bam
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236be679c9bc2a2f812ff382455e885c *inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_1_s.bam
eada6440c415bffc39581741c9d0a790 *inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_1_s.bam.bai
4a3d7a75593c3a87d833e05158e4f380 *inst/extdata/bam/ab1_ptena_wildtype_looking_embryo_2_s.bam
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a049fec3b3743cdbcab988593e07fe95 *inst/extdata/bed/guide.bed
2d865f43e37fb89160b910b38bf2d5d6 *inst/extdata/cntnap2b_test_data.fastq.gz
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25956b49d20dd443e4ce9ca7e943796e *inst/extdata/gol_F1_clutch_1_embryo_1_s.bam.bai
15010247fef191cf1d68d54cd20677da *inst/extdata/gol_F1_clutch_1_embryo_2_s.bam
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853c55081cbbc183fc46976430fa650e *inst/extdata/gol_F1_clutch_1_embryo_3_s.bam
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9e6c0eb2312197f90d0b2f352dda6b10 *inst/extdata/gol_F1_clutch_1_embryo_8_s.bam
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672eab0fa40051a31a81c9c174670eb8 *inst/extdata/gol_F1_clutch_2_embryo_4_s.bam
1b157a9c4b418311efc6caabec3cfa38 *inst/extdata/gol_F1_clutch_2_embryo_4_s.bam.bai
89b05c3e000a2e938ea38a1f90366ac2 *inst/extdata/gol_F1_metadata.txt
01243899f4f39295d5efa23b382c3949 *inst/extdata/gol_F1_metadata_small.txt
a8ef6a3063c96abb61e28f05667eb361 *inst/extdata/metadata/metadata.xls
dcc5845212d1e1b64d1956793fb683f9 *inst/extdata/ptena_GRCHz10_ref.rda
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0ae46988d1e30c47ba99181533ddab5b *man/CrisprRun-class.Rd
8eb0182c491a8749faac81194edc19b5 *man/CrisprSet-class.Rd
072ae5bbccf5fdf5a6546593b4c4c542 *man/abifToFastq.Rd
2fecc12d4d88f7079d6542183033ea88 *man/addClipped.Rd
85383eb6bf0138a6ef4f442c2f336ef6 *man/addCodonFrame.Rd
8b9c911d98568eff9108d8c8421e237f *man/alleleLabelsHelpers.Rd
d3798c03966150ee8a59c725dbd1e90f *man/alleles.Rd
80a0e82aa78e45caab2b8b94775d12f2 *man/alns.Rd
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d9053ebd495fe64e7b2dde3a2264c72e *man/arrangePlots.Rd
0b5af4e54758b4e593ba36df727cb578 *man/barplotAlleleFreqs.Rd
51acc2ced179b1a38bb1053ef49f7b7b *man/collapsePairs.Rd
a56e8c7b89af71a333f00b1de0742f56 *man/consensusSeqs.Rd
b2dc2029c182450e1390f9bd993c25a9 *man/dispatchDots.Rd
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e403c65712ea64e4d7a61eed73bdbe01 *man/explodeCigarOpCombs.Rd
33eecd97c644df926a7a956cfcb71351 *man/findChimeras.Rd
00e0e235388ea4e06cab13a33d94c526 *man/findSNVs.Rd
58aa85758f77adf3e9ed2c620e49c152 *man/getAxisCoords.Rd
5e3976dca010dd914bc66b628a03f379 *man/getChimeras.Rd
c431736bee7350c5830bd8c0e695f479 *man/getInsertionsTable.Rd
57a5eca803c6dfaee48ac219ffcad0d6 *man/gol_clutch1.Rd
1b359634aaca96c38169d26f82e282da *man/indelCounts.Rd
eb58b0bde8fdafe0884305814b3b09b9 *man/indelLabels.Rd
a2cb645c7536322268bc007b115db7bb *man/intersperse.Rd
24ddc0d007cc0d1124a0d4666c4d6dc2 *man/makeAlignmentTilePlot.Rd
87ef5dd3049e95ea9796060a2c78fd3a *man/mergeChimeras.Rd
fbfc267d85c6a496cf5f53fa768194fd *man/mergeCrisprSets.Rd
dedccfdd24ddfceea50359b2a0d41775 *man/mismatchLabels.Rd
9d6e47aa921e2d0b599eb74f6a6edcc0 *man/mutationEfficiency.Rd
6fb2d3bf5d42d08bb419aaad65e6093a *man/narrowAlignments.Rd
a852194f1fb70288283bca9ae3bf484c *man/plotAlignments.Rd
af3b4343e8c4741388c3cf7a526e3b24 *man/plotChimeras.Rd
9c8c1cecbd11099d88928260e37c1e30 *man/plotFreqHeatmap.Rd
40c46dc9ff51788f542d9f7c81abbf22 *man/plotVariants.Rd
96d8ff2e537f8da58b65c01ecbf4b884 *man/rcAlns.Rd
33594e63887f604c87eb36a855a3c462 *man/readTargetBam.Rd
ae86dbd3f35a3502b4716c5a82224c88 *man/readsByPCRPrimer.Rd
f97bb88836f60a16265d71da094fdba0 *man/readsToTarget.Rd
60b2e27a98854780de8f76b406fa27bf *man/refFromAlns.Rd
f7b14a95a2eecc31fb445a98a37df560 *man/reverseCigar.Rd
f07f2f2cc5f59b8d77e532ede6b64e49 *man/rmMultiPCRChimera.Rd
019e6005e7e1fe52fadaac20cf6342c3 *man/selectAlnRegionsHelpers.Rd
0b13786f612ef5b6884b07f9143680b9 *man/selectOps.Rd
9ea75391e4d1b6d4ca32e39009bf1db2 *man/seqsToAln.Rd
6dbdcc710f9a5b048a1eaaf957bc9b49 *man/setDNATileColours.Rd
c222f4176a4722b04e628608f4e20e4a *man/setMismatchTileColours.Rd
7b13704ae35ff30cdf11a7a65a655f3b *man/transformAlnsToLong.Rd
301cd2ffcae50ea6709370f393380d98 *man/variantCounts.Rd
9094ce538c6997c3cfb1efb4d62f7cdd *man/writeFastq.Rd
51b301187edaf2e23a0b7528fc979736 *tests/testthat.R
327ba130c50ade1a138e1d9439e24588 *tests/testthat/test-accessors.R
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b9d92881edc72c4094b8b8a5beb572c0 *tests/testthat/test-utils.R
97b178ef8b41c39fda196f63d04ebe62 *vignettes/user_guide.Rmd
