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utr.annotation  

Annotate Variants in the Untranslated Regions
View on CRAN: Click here


Download and install utr.annotation package within the R console
Install from CRAN:
install.packages("utr.annotation")

Install from Github:
library("remotes")
install_github("cran/utr.annotation")

Install by package version:
library("remotes")
install_version("utr.annotation", "1.0.4")



Attach the package and use:
library("utr.annotation")
Maintained by
Yating Liu
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-07-01
Latest Update: 2021-08-23
Description:
A fast, user-friendly tool for annotating potential deleterious variants in the untranslated regions for both human and mouse species. Y Liu, JD Dougherty (2021) .
How to cite:
Yating Liu (2021). utr.annotation: Annotate Variants in the Untranslated Regions. R package version 1.0.4, https://cran.r-project.org/web/packages/utr.annotation. Accessed 04 Dec. 2024.
Previous versions and publish date:
1.0.3 (2021-07-01 09:30), 1.0.4 (2021-08-23 08:40)
Other packages that cited utr.annotation R package
View utr.annotation citation profile
Other R packages that utr.annotation depends, imports, suggests or enhances
Functions, R codes and Examples using the utr.annotation R package
Some associated functions: checkIfGainOrLoseAfterAlt . checkIfGainOrLoseAfterAltOneVariant . checkIfLostCodonAfterAlt . checkIfLostCodonAfterAltOneVariant . checkIfRefMatchAndAltFragment . checkInputValid . concatenateAnnotationResult . countDNAPattern . countDNAPatternInAlt . countDNAPatternInAltOneVariant . countDNAPatternOneVariant . createEnsDbFromAH . getAltSequence . getCodon . getCodonInAlt . getCodonInAltOneVariant . getCodonOneVariant . getEnsembl . getFeatureFromInfo . getKozakPWM . getKozakScore . getKozakScoreOneVariant . getLatestEnsemblVersion . getOrgName . getRegionsForDiscretePos . getSeqTable . getTSSKozak . getTSSKozakOneVariant . getTranscriptIds . getTranscriptIdsForCodonVariants . getTranscriptIdsForOneCodonVariant . getTranscriptIdsForOneTSSKozakVariant . getTranscriptIdsForOneUTRVariant . getTranscriptIdsForTSSKozakVariants . getTranscriptIdsForUTRVariants . getTranscriptIdsOneVariant . getTrasncriptsRegions . get_conservation_scores . initUTRAnnotation . init_backend . inverse_transform . one_hot_encode . partitionVariantFile . predictMRL . predictMRLInAlt . predictMRLInAltOneVariant . predictMRLOneVariant . queryEnsemblInfo . readVCFData . readVariantData . runUTRAnnotation . splitRowsIfMultiFeature . validateTranscripts . 
Some associated R codes: conservation_scores.R . get_genome_db.R . read_data.R . run_annotation.R . utr5_mrl_prediction.R . utr_analysis.R .  Full utr.annotation package functions and examples
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