38cb8aa8199b1192e04ac2963734e297 *DESCRIPTION
f5487f0e90e411fc5c3be3a1f6d503a5 *LICENSE
720397a520190239c6fd684d0fc32e0d *NAMESPACE
00e1543d4b5539abb47b86a76c59a13d *R/AllGenerics.R
2180f556f82b76b77208d5cd34784bd5 *R/GuideSet-class.R
a7c10a7cdee90eaa55ac4c6f3d281355 *R/GuideSet2DataFrames.R
ae2cd2f34d66cd235a8e6eaf2db0116b *R/PairedGuideSet-class.R
55bb78c9e1e38e192e15cab0c8cf7802 *R/TxDb2GRangesList.R
ed9a9530c47f99495b47386afe1ad6cd *R/addCompositeScores.R
bb43ffc474528d36538077f3984f2452 *R/addConservationScores.R
d2bb614b68d32fbaec7d8394bdc8ad4c *R/addDistanceToTss.R
4c61fd6963d2599848c5a73b7d417ca7 *R/addEditedAlleles.R
6a9c8a3338086158561448bc08f1ac83 *R/addEditingSites.R
5b594d7dbe7a56a60217ed88726f5b5f *R/addExonTable.R
74a7ea9e7a4b1feeea1ba41652d3e9ea *R/addGeneAnnotation.R
1ee70de746e32dd505eda88f505a8a30 *R/addIsoformAnnotation.R
074ab626b2aa5cbe42ec0fcfc338a5dc *R/addNtcs.R
5e04baa3dfa987f40c3fa5e972741cd3 *R/addOffTargetScores.R
eadb86d21e29743b61c2da5ca61a0cbf *R/addOnTargetScores.R
13ea4e422d15dba52583104c1bd7887a *R/addPamScores.R
a3b570ddc8e9b0034b73e4e5da162f68 *R/addPfamDomains.R
be2ec44551ee93678d2ac0781733fb4c *R/addReinitiationFlag.R
d413aa0c88154cd4c08b9c3a6a56e7eb *R/addRepCoordinates.R
4cf5868383e32d5106f936991aac588e *R/addRepeats.R
f779cda52b755865370099650c94776a *R/addRestrictionEnzymes.R
3e90c9a8c961ed87389bf9753f8272ab *R/addSNPAnnotation.R
3c5313dfcc2d142c188d13d0f0cd75fe *R/addSequenceFeatures.R
9b48d31071a1edda80f37fcb455bbb46 *R/addSpacerAlignments.R
139468505f68f43d2ba7a72926e5609a *R/addSpecificityProxyScore.R
cdbc419bf3f0c27106120c025302cff4 *R/addTssAnnotation.R
418e52bb5b2efd69e07b571ded5e15b5 *R/addTxTable.R
748ad91f6abb143dd51436d819b2c19d *R/completeSpacers.R
4b59d88bd24bde0456ea31172a31d3eb *R/data.R
6214c8ef2d949449c7a883d90b993a13 *R/designCompleteAnnotation.R
5784c5819ddc561345f4e355e849aab5 *R/findSpacerPairs.R
7ad8cc2a19136dfcf1503176e891fde0 *R/findSpacers.R
bdf31f6cab04b7f01c60ccf4ca9f8fe6 *R/getConsensusIsoform.R
b3faf8104b7ddca74f3725115e7ab108 *R/getMrnaSequence.R
4f284810a2b55a6c1c51dc610c25c42e *R/getTssObjectFromTxObject.R
63885a1fcdb2bf5f49065ea638b4afec *R/getTxInfoDataFrame.R
c8dcf14788b085384491128ac4153701 *R/opsDesign.R
22280cb33b1611341eddf93e518484c6 *R/queryTxObject.R
cbda5ae42bf4a5dbf4bad8584be9265a *R/rankSpacers.R
d5bce82ff522e75b18f674756366a520 *R/removeMultiGeneTargeting.R
ee8b8309421fc793c20c24fba85a1560 *R/utils.R
353d62aa6eec3e21494152d93927eed8 *README.Rmd
238d3dfb8787cc2611655489a0bfe61a *README.md
0a41fcfc8a24d13cdd3d6a1e3ea9e4d8 *build/vignette.rds
33af56d65c3a1a16b23acb10d2b98729 *data/grListExample.rda
b0ccf8be6165645ba514ed9a8ace412f *data/grRepeatsExample.rda
63279fa615eeb841cf94fd433b2a3839 *data/guideSetExample.rda
4a441f398b67b1ce19df950611b68a1f *data/guideSetExampleFullAnnotation.rda
6d74d51cf75c5a60e633dec86c56e01b *data/guideSetExampleWithAlignments.rda
2994295b8e0650cb3d7b199210e0f451 *data/snpObjectExample.rda
b773765cb8f3ebac7b613a007d319fbd *data/tssObjectExample.rda
0f8996589d0460fbf6d58cd1a67c673d *inst/CITATION
0c8c5f60d9e8ee195bd0d48957131b37 *inst/NEWS.Rd
1eddff6785d09c109bfbfab983ef4535 *inst/TODO.txt
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7eab2eaf275621c733728af4f7b3df8e *inst/doc/intro.html
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5a6bc373093e36f7e88a4af8f25d834d *inst/examples/example_cas12a.R
5591134fe0ec15c1fe69b0450e9b878f *inst/examples/example_cas13d.R
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3f2d758bbd776f8e9a2c829d0f7102d9 *inst/examples/example_multi_species.R
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a8a645875f16f1d1c39bcef3eee55724 *inst/examples/examples.Rmd
6858667e94fdde442b6c212b973c5db5 *inst/examples/ops.R
730d5703550204a6cb60602cfcb757e4 *inst/extdata/common_snps_dbsnp151_example.vcf.gz
29b831dcce43efa208537d2444c183fc *inst/extdata/common_snps_dbsnp151_example.vcf.gz.tbi
12598328fcee8e39246d0f775d9a8cc9 *inst/fasta/chr12.fa
3ed5c97e7319a44c642c47cd67c056a4 *inst/paired/papers/cas_FokI.pdf
a2cc86c22fdd332ad7bb15547ac4af70 *inst/paired/papers/double_nicking_d10A.pdf
0eb39176b4db96d47716a4635efafd67 *inst/scripts/generateFastaExample.R
f51308d2e0ab8c00a1ba07a84ab767de *inst/scripts/generateGuideSet.R
7f283ad40f0293ca18e7ae9bade98aa1 *inst/scripts/generateGuideSetFullAnnotation.R
c979c0aebc27779ec1c20bf8c9e02f44 *inst/scripts/generateRepeatsData.R
38353ff64726abe3ee80126797322c89 *inst/scripts/generateSnpsExample.R
17578e1dcefac7b3cab8dff4417ef744 *inst/scripts/generateTssData.R
382abbd01c1453f2906ecdec6bb94e5b *inst/scripts/generateTxDbData.R
03bf063f2b5111830299f80603259e05 *inst/scripts/generateVcfExample.R
90792e61397982c980676720c3b6f287 *inst/utils/array.R
95d8a8aa655f217db90c99b82964d86d *inst/utils/beFigure.R
e0b699b0840ef06bcc69ff7b7ac3973d *inst/utils/celltracker.R
d73e1b592fc9dab4e99315dd41493a18 *inst/utils/differential.R
097450de31d3cdf73ec3a748fc549338 *inst/utils/dualGuides_equalization.R
50bec9e4bf16c98583efb42cdd00d612 *inst/utils/dualGuides_normalization.R
2ce641cc7966b0e3a7dcaf408e98b917 *inst/utils/dualGuides_transformations.R
df91d04f6236835decddb55b05d1cdc8 *inst/utils/dualGuides_vizualizations.R
5088d61906bb6d7afdd296f357115ffa *inst/utils/getCrisprBlissScores.R
81c80f2ce3eb62de15278a9825e6a8af *inst/utils/getGeminiScores.R
fbb752b93108a1873cffa6d6538c894d *inst/utils/minimap2.R
66513ae948b56c0484082c18e45a496e *inst/utils/normalization.R
198f3171eba9ae394222c43ea7bbe6f6 *inst/utils/pca.R
205c9c5950068be50cebd33ba5eb0740 *inst/utils/qc.R
54e7756b369bd3ce9b096051041135e1 *inst/utils/tiling.R
c8092a786bf1a057a4d58387b6230892 *inst/utils/transformations.R
f8e694bac1d6fb5bc4331f876cf6590b *inst/utils/utils.R
3e88a3da7f5bb23ba6d33ce75ed8c0f1 *inst/utils/viz.R
0cebb85c9eac59d5a923665f1ca57de3 *man/GuideSet-class.Rd
aa728efd5de32ade69baab85a08b15b9 *man/GuideSet2DataFrames.Rd
ccc665eb21952268885f13a906e587e7 *man/PairedGuideSet-class.Rd
b2867d1160a196077eab14ba99af8642 *man/TxDb2GRangesList.Rd
feaa91422becd002ecb48a34a11a84d8 *man/addCompositeScores.Rd
fb0b9e40b323c2ae293025416cfcf1de *man/addConservationScores.Rd
79e8eec275bb5a58b207b3fbc0db1ae4 *man/addDistanceToTss.Rd
88fb9269c951da9063f82e31ea28820e *man/addEditedAlleles.Rd
daf98761009f49a8f64b00a8f7c86cdd *man/addEditingSites.Rd
d7273458cd8198be1260987534805af8 *man/addExonTable.Rd
6c9338fa506c6d26e8a9780e2a54f54d *man/addGeneAnnotation.Rd
c64910cb414bf76d2b8b32755ec98435 *man/addIsoformAnnotation.Rd
3f7968e3e9b005992acd4e76d252e39f *man/addNtcs.Rd
7ee55948731eec86a417b6f136bb2283 *man/addOffTargetScores.Rd
e4c5df7405a61147e4a63fe494f53247 *man/addOnTargetScores.Rd
93c11cf7f07acf5be531b06e9b4de48d *man/addOpsBarcodes.Rd
d66b5f9afdcd82e7ff5deafef5a169da *man/addPamScores.Rd
321dae3841f7b811f07ce54e426d7274 *man/addPfamDomains.Rd
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bc211e1d8a5f7c48dc02811e6504a468 *man/addRepCoordinates.Rd
8fd8faa53441b4674d3e6ff5d88ac920 *man/addRepeats.Rd
46192f913b3f0ffa3309e81af8318670 *man/addRestrictionEnzymes.Rd
e78a1f78c0dd5bc2c031a330469cff23 *man/addSNPAnnotation.Rd
ca540a2b9f2f70d92bcfa0a281edcb97 *man/addSequenceFeatures.Rd
7fd0221ecd79f63d439d84e1f625a6fe *man/addSpacerAlignments.Rd
38e6f823431535e2b9b4be442e775ac0 *man/addSpecificityProxyScore.Rd
59eba310278f7e17d8620b9cea0487ab *man/addTssAnnotation.Rd
df038a63f541410f2fb763b0260d953b *man/addTxTable.Rd
9d206a7de8321ef94b7da8da5d6b861e *man/completeSpacers.Rd
78ef04aff1aace3898e930748ef91278 *man/convertToMinMaxGRanges.Rd
d4bf58f5da290be80767a41b1cbcbd37 *man/convertToProtospacerGRanges.Rd
021bb69afe759519463bd8ac94027281 *man/designCompleteAnnotation.Rd
622e1599af6a1e76238d58837069ce66 *man/designOpsLibrary.Rd
0868c918004ba6585bfe70b920677a55 *man/findSpacerPairs.Rd
8235a1f533e5571b6b3c28902f9a2a5e *man/findSpacers.Rd
6b80ca9442ff34e0e2ba990eb6a96308 *man/flattenGuideSet.Rd
1be1e0ef9eecdf4fd63c09550c9ea59e *man/getBarcodeDistanceMatrix.Rd
667acc50bfebb9b5aabfb282524ff789 *man/getConsensusIsoform.Rd
36f12d4c9b344fb7f957010f094929f3 *man/getMrnaSequences.Rd
1fa2537cc9fd4e3c8fefc5335dc4d899 *man/getPreMrnaSequences.Rd
632568966f0785e30151f3c07a90a33c *man/getTssObjectFromTxObject.Rd
e31f949a5158775b54befc053c80b976 *man/getTxDb.Rd
a742653aae2f3ea15d6f1958681de26e *man/getTxInfoDataFrame.Rd
610163aa7873233d0c767626f6c90aba *man/grListExample.Rd
d7e48ab204ea42fe984f7659fa0f5179 *man/grRepeatsExample.Rd
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5bcbd2ae5273f3f725e602d5ab2dec38 *man/guideSetExampleFullAnnotation.Rd
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3b3b97d33a8f5ae23641990e87c2a1ee *man/queryTss.Rd
e7e2c81ab2a6b76c303bbf1692ad61d4 *man/queryTxObject.Rd
7f8c66bfce48e69547bfdbdf677482a3 *man/rankSpacers.Rd
64446b3232e2d772327de50c70482602 *man/reexports.Rd
27809e6f82b98f3c7d864f2f4d20b11b *man/removeRepeats.Rd
da35acfee7d60d77d17c47009182c0a9 *man/removeSpacersWithSecondaryTargets.Rd
47c719e72d99694884494031a1970659 *man/snpObjectExample.Rd
31fdaec69596a74786161878c50cebf8 *man/tssObjectExample.Rd
5e2dee4363e937564dfc5d5aa897c1aa *man/updateOpsLibrary.Rd
a8190552b4bb38b583058e36154245c6 *man/validateOpsLibrary.Rd
2e6d70d17f8ba9cc89885afb02d063d2 *tests/testthat.R
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4a30a6ce03aadc61e0f4001d5af75b18 *tests/testthat/test-completeSpacers.R
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ee178d3aae063b831c7a3523011be6d7 *tests/testthat/test-queryTxObject.R
b2f663cce2a03b743d55b96fa9f73a92 *tests/testthat/test-rankSpacers.R
9390a4f33e5b1d8c831087e7f5dc60bb *vignettes/baseEditing.Rmd
521752df5ed35d281b07d711c8bd7e63 *vignettes/figures/paired.pdf
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174da069b2f1e0e7165a392122af7c87 *vignettes/figures/paired.svg
e7f1846117b771de5ae21792827f3d32 *vignettes/figures/paired_simplified.pdf
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41da340e39c80c851284701945d909e5 *vignettes/figures/resave.sh
43663af5e1dca20f839cd8b7638cced1 *vignettes/intro.Rmd
4726ec1fd67e6758673f72cb946d2d10 *vignettes/references.bib
