9c5a4c7844e04ba116914f3811550ab0 *DESCRIPTION
6623d2a44480d5f289bac400844ce0e0 *NAMESPACE
7b772ffb979ee5ec89dd979b56320fe9 *NEWS.md
42ebe313090b648755b3e160b0640c24 *R/conservation_scores.R
a370785a29c0a6dae5423d2454532403 *R/get_genome_db.R
45b56ecc512207c5df02569ea37af205 *R/read_data.R
43d925019e98fe29f23a0fc2e7bacd6e *R/run_annotation.R
0d1cad519230ea85b30c24e01377e765 *R/sysdata.rda
60ac6b2b16085e5226cad4856146ef62 *R/utr5_mrl_prediction.R
0b90ce1fd1eabf5282111054deb9bb95 *R/utr_analysis.R
459390261ea296b357cc06dd76bba9bf *README.md
6ca6638c6e42b5f025310f91384ddb46 *build/vignette.rds
a9d77e4f56f0d7fa3121337871cef032 *inst/doc/introduction.R
8702c5cf20535f0d0869ff2bd4f1e375 *inst/doc/introduction.Rmd
09fd51cfa0e5212316f34d71f771dacd *inst/doc/introduction.pdf
ad3abe4cd9edd2d9b72867bc8783a8c5 *inst/extdata/Conservation_scores/hg38.phastCons100way.bw
81479257d615293917e76642b7ccbbc7 *inst/extdata/Conservation_scores/hg38.phyloP100way.bw
58ba52160c74f2eec4b5c907c9073bde *inst/extdata/annotated_variants_sample.csv
43261f42fb5b9ab1522ffaf0bb6eba1a *inst/extdata/runtimes_upto_10000_vars.rds
e0b779b4a4c06d424bfb7d104d67356c *inst/extdata/variants_sample.csv
fc9bbc2c72d3dd387644251a4bf6bcc6 *man/checkIfGainOrLoseAfterAlt.Rd
ae0ab8d408bdfec7ea0ad70a1be92601 *man/checkIfGainOrLoseAfterAltOneVariant.Rd
0b168034e83a70098c85da2efd46c27f *man/checkIfLostCodonAfterAlt.Rd
c850614ff3a92792fc616ee5cc0e9ef8 *man/checkIfLostCodonAfterAltOneVariant.Rd
ec370dc01fe705c9a84b4b3e5ce2f000 *man/checkIfRefMatchAndAltFragment.Rd
61b766d8bba732458fb1632ef3dcbbb7 *man/checkInputValid.Rd
e94d84e66c1cd4050585148bf21ea6be *man/concatenateAnnotationResult.Rd
5c0de4a47c96c11adc83186750d05c17 *man/countDNAPattern.Rd
72870b7d09d8895cc8f258abcebfe9e7 *man/countDNAPatternInAlt.Rd
d34f2709312ca46db83c383e78cfb997 *man/countDNAPatternInAltOneVariant.Rd
278cff2bcf6abe35bf0fb26dcb94f794 *man/countDNAPatternOneVariant.Rd
6adbca5442259ae377fe4785f19145ec *man/createEnsDbFromAH.Rd
e3023cd1d76476fb577b7977136c7db2 *man/getAltSequence.Rd
9e82e5d2905dd1876b09c45c8008ceaf *man/getCodon.Rd
70374ad12628580f2a312614e6de3ae0 *man/getCodonInAlt.Rd
908471b57b2fd3562ac049f520c513c1 *man/getCodonInAltOneVariant.Rd
4f5ef5777aeec064d4814e33893048f1 *man/getCodonOneVariant.Rd
7acb9ebce203fe1f2804a97435b39d2c *man/getEnsembl.Rd
e44461d452fd81f1048cdfa34e93d408 *man/getFeatureFromInfo.Rd
1b0d3c5124968a7338eabd22f242581a *man/getKozakPWM.Rd
9886c69fda1eacc8a382a54b89836e36 *man/getKozakScore.Rd
75bcd071116602f1a93b414016e669c3 *man/getKozakScoreOneVariant.Rd
41672d2b3dd483aa2475cdfd34e32ef9 *man/getLatestEnsemblVersion.Rd
1faa21ac94c3465c017dbf7cb66c8eed *man/getOrgName.Rd
b55f818f615eee6d6874f382e8ff48c3 *man/getRegionsForDiscretePos.Rd
001c8be4934d36c7cd89629ee42f1749 *man/getSeqTable.Rd
f84e536ac88b9987273e345fd5825460 *man/getTSSKozak.Rd
db59081b94e3e280bd13e77e4e9d6608 *man/getTSSKozakOneVariant.Rd
ffe5d00edaf75a29e207015736ecf893 *man/getTranscriptIds.Rd
6b935ee174be75ba519960c0b4cc3a79 *man/getTranscriptIdsForCodonVariants.Rd
713a766f2b7d535c8b7e58da896542fb *man/getTranscriptIdsForOneCodonVariant.Rd
a35158dd2e15960340a8d0ad2c41285b *man/getTranscriptIdsForOneTSSKozakVariant.Rd
d756176548271cca569c3f77b8fe64c9 *man/getTranscriptIdsForOneUTRVariant.Rd
9c88d82af1073172a74867d3e074ad43 *man/getTranscriptIdsForTSSKozakVariants.Rd
34494fa8aec92c4306129f0df72b0ef7 *man/getTranscriptIdsForUTRVariants.Rd
dee21210be9be0ba3ff4852297d9da5e *man/getTranscriptIdsOneVariant.Rd
ea4ff0f3a541860405369e912f729c16 *man/getTrasncriptsRegions.Rd
0b5e70b863b383a3fb5c1a2cf8192a07 *man/get_conservation_scores.Rd
d574cbd6f86c56636634c692d26945dc *man/initUTRAnnotation.Rd
26778e8c2f09f717772090ff057678cf *man/init_backend.Rd
5663cf180526b0b33b8ffd3f0ce4d0ca *man/inverse_transform.Rd
576e16b748eff663823d04bf818c323f *man/one_hot_encode.Rd
b102a5113f0ed42ec75de3f62669f4ac *man/partitionVariantFile.Rd
7a6ccab0c3eb9281545198d4cd6ac14a *man/predictMRL.Rd
ef5d6acf4bb076c85c8ea9d915ffd3d2 *man/predictMRLInAlt.Rd
c3418ee4ec7d5a9b7e3d430a8842af35 *man/predictMRLInAltOneVariant.Rd
fc71234eb5cd646285739788fe8c5557 *man/predictMRLOneVariant.Rd
046464c3688a8cca5288a6063325203b *man/queryEnsemblInfo.Rd
072bc5f250b92e43cd8f66d975702b45 *man/readVCFData.Rd
4c8bed849b789c9213042acc59e6266f *man/readVariantData.Rd
b3823ff152832310f889b324f8a635d7 *man/runUTRAnnotation.Rd
8971fac3161e4699d0a7e2acf3448fb7 *man/splitRowsIfMultiFeature.Rd
97cb7892872181d464ceec68587b6bfb *man/validateTranscripts.Rd
c46104462485e24f04ef495229985a93 *tests/testthat.R
c13b4ea9fd52e0a447cd8aa5887d9cdb *tests/testthat/test-conservation_scores.R
9c04235df188efd017a09797e2f5f4b9 *tests/testthat/test-get_genome_db.R
a0a42e194f936d8e176f036e0b12d3b5 *tests/testthat/test-read_data.R
25db59783d3e0dd1f93e7efd3efd59d3 *tests/testthat/test-run_annotation.R
edfc1e14e13096cc353dc56ca47e7751 *tests/testthat/test-utr5_mrl_prediction.R
824178699765da4dca4ad4e4e0234891 *tests/testthat/test-utr_analysis.R
ad3abe4cd9edd2d9b72867bc8783a8c5 *tests/testthat/testdata/Conservation_scores/hg38.phastCons100way.subset.bw
81479257d615293917e76642b7ccbbc7 *tests/testthat/testdata/Conservation_scores/hg38.phyloP100way.subset.bw
cffcce973bd9f6b43eae10846522d4f4 *tests/testthat/testdata/kozakPWM.rds
f1f42f8073c0fc9388dc4fcad72be877 *tests/testthat/testdata/partition_example.csv
9f94b6614fa0c00296d5ba331fd6dc73 *tests/testthat/testdata/uAUG_repressive_strength.csv
6f7a9d9d463aa98669eb0f0cb18f1712 *tests/testthat/testdata/variants_no_feature.csv
0ddbd27e25e55a97b45b41a04f6a2dfc *tests/testthat/testdata/variants_sample.csv
7610eb74b546cb1310765a7240e7f955 *tests/testthat/testdata/variants_sample_results.csv
b0df6a698f46c0fced1a9bedb41f9721 *tests/testthat/testdata/variants_sample_results_no_mrl.csv
b0ae9f2b5d26fd63aa90e8e6cd4ddb5b *tests/testthat/testdata/variants_sample_results_utr5_seqs.csv
8ef4ed34ca5d9e8511cd567f8d903674 *tests/testthat/testdata/variants_sample_with_trans.csv
8087befe08a1566b74f802ef34921852 *tests/testthat/testdata/vcf_multialts.csv
debbbf213f1d6c1d1e829b3e9693b908 *tests/testthat/testdata/vcf_multialts.vcf
6207075484755f7b962883010605c9ac *tests/testthat/testdata/vcf_multialts_and_multigenes.csv
05b6f5b070c329ab72b0c6a78cee537e *tests/testthat/testdata/vcf_multialts_and_multigenes.vcf
b75787f2f5d6633d37067fedf3a41f29 *tests/testthat/testdata/vcf_multialts_and_multigenes_splitted.csv
a5c90975f4486f171b9f9b243d0cf111 *tests/testthat/testdata/vcf_multialts_splitted.csv
62d5188d89a09211cb2d5fb52d92d4c6 *tests/testthat/testdata/vcf_multigenes.vcf
f4f6e3e831e9c1b6df9b6150f6dba8b5 *tests/testthat/testdata/vcf_variants.vcf
dc87033b55c3a9116f9ca7dffd794775 *tests/testthat/testdata/vcf_variants_results.csv
90da11745f84af00a5af828c764a2fec *tests/testthat/testdata/vcf_variants_results_no_mrl.csv
8702c5cf20535f0d0869ff2bd4f1e375 *vignettes/introduction.Rmd
