Files in utr.annotation
Annotate Variants in the Untranslated Regions
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
R/sysdata.rda
R/run_annotation.R
R/get_genome_db.R
R/read_data.R
R/utr5_mrl_prediction.R
R/utr_analysis.R
R/conservation_scores.R
inst/doc/introduction.pdf
inst/doc/introduction.R
inst/doc/introduction.Rmd
inst/extdata/annotated_variants_sample.csv
inst/extdata/runtimes_upto_10000_vars.rds
inst/extdata/variants_sample.csv
inst/extdata/Conservation_scores/hg38.phastCons100way.bw
inst/extdata/Conservation_scores/hg38.phyloP100way.bw
build/vignette.rds
tests/testthat.R
tests/testthat/test-get_genome_db.R
tests/testthat/test-utr5_mrl_prediction.R
tests/testthat/test-utr_analysis.R
tests/testthat/test-read_data.R
tests/testthat/test-conservation_scores.R
tests/testthat/test-run_annotation.R
tests/testthat/testdata/variants_sample_results_no_mrl.csv
tests/testthat/testdata/vcf_variants.vcf
tests/testthat/testdata/variants_sample_results_utr5_seqs.csv
tests/testthat/testdata/vcf_multialts_and_multigenes.csv
tests/testthat/testdata/vcf_multigenes.vcf
tests/testthat/testdata/variants_no_feature.csv
tests/testthat/testdata/vcf_multialts_splitted.csv
tests/testthat/testdata/vcf_variants_results.csv
tests/testthat/testdata/kozakPWM.rds
tests/testthat/testdata/partition_example.csv
tests/testthat/testdata/vcf_multialts_and_multigenes_splitted.csv
tests/testthat/testdata/vcf_variants_results_no_mrl.csv
tests/testthat/testdata/uAUG_repressive_strength.csv
tests/testthat/testdata/variants_sample_with_trans.csv
tests/testthat/testdata/vcf_multialts.csv
tests/testthat/testdata/vcf_multialts_and_multigenes.vcf
tests/testthat/testdata/variants_sample.csv
tests/testthat/testdata/variants_sample_results.csv
tests/testthat/testdata/vcf_multialts.vcf
tests/testthat/testdata/Conservation_scores/hg38.phyloP100way.subset.bw
tests/testthat/testdata/Conservation_scores/hg38.phastCons100way.subset.bw
vignettes/introduction.Rmd
man/checkIfLostCodonAfterAltOneVariant.Rd
man/countDNAPatternInAltOneVariant.Rd
man/checkInputValid.Rd
man/predictMRLOneVariant.Rd
man/getFeatureFromInfo.Rd
man/getKozakPWM.Rd
man/initUTRAnnotation.Rd
man/getTranscriptIds.Rd
man/concatenateAnnotationResult.Rd
man/getCodon.Rd
man/getTSSKozakOneVariant.Rd
man/countDNAPatternOneVariant.Rd
man/getTranscriptIdsForCodonVariants.Rd
man/getOrgName.Rd
man/createEnsDbFromAH.Rd
man/getCodonOneVariant.Rd
man/getRegionsForDiscretePos.Rd
man/getCodonInAltOneVariant.Rd
man/getKozakScoreOneVariant.Rd
man/getTranscriptIdsForOneCodonVariant.Rd
man/getEnsembl.Rd
man/countDNAPattern.Rd
man/countDNAPatternInAlt.Rd
man/getSeqTable.Rd
man/splitRowsIfMultiFeature.Rd
man/inverse_transform.Rd
man/readVCFData.Rd
man/predictMRLInAltOneVariant.Rd
man/getKozakScore.Rd
man/getTranscriptIdsForOneTSSKozakVariant.Rd
man/get_conservation_scores.Rd
man/one_hot_encode.Rd
man/checkIfGainOrLoseAfterAltOneVariant.Rd
man/getTranscriptIdsOneVariant.Rd
man/checkIfGainOrLoseAfterAlt.Rd
man/getTranscriptIdsForUTRVariants.Rd
man/validateTranscripts.Rd
man/partitionVariantFile.Rd
man/getTranscriptIdsForTSSKozakVariants.Rd
man/checkIfRefMatchAndAltFragment.Rd
man/queryEnsemblInfo.Rd
man/checkIfLostCodonAfterAlt.Rd
man/getCodonInAlt.Rd
man/init_backend.Rd
man/getTranscriptIdsForOneUTRVariant.Rd
man/getLatestEnsemblVersion.Rd
man/runUTRAnnotation.Rd
man/predictMRLInAlt.Rd
man/getTrasncriptsRegions.Rd
man/getTSSKozak.Rd
man/getAltSequence.Rd
man/readVariantData.Rd
man/predictMRL.Rd
