| checkIfGainOrLoseAfterAlt | Check if the number of uAUG, ployA signal, or Kozak in UTR... |
| checkIfGainOrLoseAfterAltOneVariant | Check if the number of uAUG, ployA signal, or Kozak in UTR... |
| checkIfLostCodonAfterAlt | Check if the codon lost after alt. |
| checkIfLostCodonAfterAltOneVariant | Check if the codon lost after alt for one variant. |
| checkIfRefMatchAndAltFragment | Check if the nucleotides in Ref column match the actual... |
| checkInputValid | Check if the variable table is a valid for UTR annotation |
| concatenateAnnotationResult | Concatenate annotation result files into one file |
| countDNAPattern | Count the number of DNA pattern for each transcript, and... |
| countDNAPatternInAlt | Count the number of DNA pattern in the altered sequence of... |
| countDNAPatternInAltOneVariant | Count the number of DNA pattern in the altered sequence of... |
| countDNAPatternOneVariant | Count the number of DNA pattern for one variant |
| createEnsDbFromAH | Create a EnsDb database file from AnnotationHub |
| getAltSequence | Check if Ref matches the actual sequence, if so then return... |
| getCodon | Get the codon sequence for transcripts in transcriptIdColumn. |
| getCodonInAlt | Get the altered codon sequence for transcripts in... |
| getCodonInAltOneVariant | Get the altered codon sequence for transcripts in... |
| getCodonOneVariant | Get the codon sequence of transcripts in transcriptIdColumn... |
| get_conservation_scores | Get conservation scores for variants |
| getEnsembl | Get Ensembl database object for the specified species |
| getFeatureFromInfo | Get feature information from INFO column of VCF file |
| getKozakPWM | Get Kozak PWM |
| getKozakScore | Calculate the Kozak score for each Kozak sequence, and... |
| getKozakScoreOneVariant | Calculate the Kozak score for each Kozak sequence, and... |
| getLatestEnsemblVersion | Get the latest Ensembl version that available by querying... |
| getOrgName | Convert species name to AnnotationHub acceptable species name |
| getRegionsForDiscretePos | Get codon region table used for getAltSequence |
| getSeqTable | Get UTR sequences of a list of transcripts |
| getTranscriptIds | Get protein coding transcript ids that overlap with each... |
| getTranscriptIdsForCodonVariants | Find the ensembl_transcript_id and codon positions for... |
| getTranscriptIdsForOneCodonVariant | Find the ensembl_transcript_id and codon postions for one... |
| getTranscriptIdsForOneTSSKozakVariant | Find the ensembl_transcript_id and kozak_positions for one... |
| getTranscriptIdsForOneUTRVariant | Find all the ensembl_transcript_id for a variant which fall... |
| getTranscriptIdsForTSSKozakVariants | Find the ensembl_transcript_id and kozak_positions for... |
| getTranscriptIdsForUTRVariants | Find the ensembl_transcript_id for utr variants genes, or cds |
| getTranscriptIdsOneVariant | Search the db to find protein coding transcript ids that... |
| getTrasncriptsRegions | Get information on transcript regions, UTRs regions, coding... |
| getTSSKozak | Get the Kozak sequence in TSS region for transcripts in... |
| getTSSKozakOneVariant | Get the Kozak sequence in TSS region for transcripts in... |
| init_backend | Create parallel backend with user specified number of CPUs |
| initUTRAnnotation | Query transcripts regions and sequences from Ensembl database |
| inverse_transform | Reverse the scaling of the predicted MRL |
| one_hot_encode | Apply one hot encode to the 100nt 5' UTR sequence |
| partitionVariantFile | Partition the variant file to run in parallel |
| predictMRL | Get the 100nt 5' UTR sequence upstream of start codon for... |
| predictMRLInAlt | Get the mutated 100nt 5' UTR sequence upstream of start codon... |
| predictMRLInAltOneVariant | Predict altered MRL for one variant |
| predictMRLOneVariant | Predict MRL for one variant |
| queryEnsemblInfo | query transcrips regions, utr sequences, and coding sequences... |
| readVariantData | Read variant file in CSV format |
| readVCFData | Read variants from a VCF formatted file |
| runUTRAnnotation | Run UTR annotation on a variant file |
| splitRowsIfMultiFeature | Split rows if the feature column(s) contains multiple items,... |
| validateTranscripts | Checking whether a transcript is valid |
