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 |
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