ORFik-package           ORFik for analysis of open reading frames.
addCdsOnLeaderEnds      Extends leaders downstream
addNewTSSOnLeaders      add cage max peaks as new transcript start
                        sites for each 5' leader (*) strands are not
                        supported, since direction must be known.
asTX                    Map genomic to transcript coordinates by
                        reference
assignAnnotations       Overlaps GRanges object with provided
                        annotations.
assignFirstExonsStartSite
                        Reassign the start positions of the first exons
                        per group in grl
assignLastExonsStopSite
                        Reassign the stop positions of the last exons
                        per group
assignTSSByCage         Input a txdb and add a 5' leader for each
                        transcript, that does not have one.
bedToGR                 Converts different type of files to Granges
changePointAnalysis     Get the offset for specific RiboSeq read width
checkRFP                Helper Function to check valid RFP input
checkRNA                Helper Function to check valid RNA input
codonSumsPerGroup       Get hits per codon
computeFeatures         Get all possible features in ORFik
computeFeaturesCage     Get all possible features in ORFik
convertToOneBasedRanges
                        Convert a GRanges Object to 1 width reads
coverageByWindow        Compute coverage for every GRangesList subset.
coveragePerTiling       Get coverage per group
defineIsoform           Overlaps GRanges object with provided
                        annotations.
defineTrailer           Defines trailers for ORF.
detectRibosomeShifts    Detect ribosome shifts
disengagementScore      Disengagement score (DS)
distToCds               Get distances between ORF ends and starts of
                        their transcripts cds'.
distToTSS               Get distances between ORF Start and TSS of its
                        transcript
downstreamFromPerGroup
                        Get rest of objects downstream (inclusive)
downstreamN             Restrict GRangesList
downstreamOfPerGroup    Get rest of objects downstream (exclusive)
entropy                 Calucalte entropy value of overlapping input
                        reads.
extendLeaders           Extend the leaders transcription start sites.
extendsTSSexons         Extend first exon of each transcript with
                        length specified
filterCage              Filter peak of cage-data by value
findCageUTRFivelen      Get length of leaders ordered after oldTxNames
findFa                  Convenience wrapper for Rsamtools FaFile
findMapORFs             Find ORFs and immediately map them to their
                        genomic positions.
findMaxPeaks            Find max peak for each transcript, returns as
                        data.table, without names, but with index
findNewTSS              Finds max peaks per trancsript from reads in
                        the cagefile
findORFs                Find Open Reading Frames.
findORFsFasta           Finds Open Reading Frames in fasta files.
firstEndPerGroup        Get first end per granges group
firstExonPerGroup       Get first exon per GRangesList group
firstStartPerGroup      Get first start per granges group
floss                   Fragment Length Organization Similarity Score
fpkm                    Create normalizations of overlapping read
                        counts.
fpkm_calc               Create normalizations of counts
fractionLength          Fraction Length
fread.bed               Load bed file as GRanges.
gSort                   Sort a GRangesList, helper.
getStartStopWindows     Get Start and Stop codon within specified
                        windows over CDS.
groupGRangesBy          Group GRanges
hasHits                 Hits from reads
initiationScore         Get initiation score for a GRangesList of ORFs
insideOutsideORF        Inside/Outside score (IO)
is.gr_or_grl            Helper function to check for GRangesList or
                        GRanges class
is.grl                  Helper function to check for GRangesList
isInFrame               Find frame for each orf relative to cds
isOverlapping           Find frame for each orf relative to cds
isPeriodic              Find if there is periodicity in the vector
kozakSequenceScore      Make a score for each ORFs start region by
                        proximity to Kozak
lastExonEndPerGroup     Get last end per granges group
lastExonPerGroup        Get last exon per GRangesList group
lastExonStartPerGroup   Get last start per granges group
longestORFs             Get longest ORF per stop site
makeExonRanks           Make a meta column with exon ranks
makeORFNames            Make ORF names per orf
mapToGRanges            Map orfs to genomic coordinates
matchNaming             Match naming of GRangesList
metaWindow              Calculate metaplot coverage of reads around
                        input GRangesList object.
numExonsPerGroup        Get list of the number of exons per group
orfID                   Get id's for orf
orfScore                Get ORFscore for a GRangesList of ORFs
overlapsToCoverage      Get overlaps and convert to coverage list
parseCigar              Shift ribo-seq reads using cigar string
pmapFromTranscriptF     Faster more secure version of
                        mapFromTranscripts
rankOrder               ORF rank in transcripts
readWidths              Get RiboSeq widths
reassignTSSbyCage       Reassign all Transcript Start Sites (TSS)
reassignTxDbByCage      Input a txdb and reassign the TSS for each
                        transcript by CAGE
reduceKeepAttr          Reduce GRanges / GRangesList
regroupRleList          Regroup rle from GRangesList
remakeTxdbExonIds       Get new exon ids
removeMetaCols          Removes meta columns
removeTxdbExons         Remove exons in txList that are not in fiveUTRs
restrictTSSByUpstreamLeader
                        Restrict extension of 5' UTRs to closest
                        upstream leader end
riboTISCoverageProportion
                        Find proportion of reads per position in ORF
                        TIS window
ribosomeReleaseScore    Ribosome Release Score (RRS)
ribosomeStallingScore   Ribosome Stalling Score (RSS)
seqnamesPerGroup        Get list of seqnames per granges group
shiftFootprints         Shift footprints by selected offsets
sortPerGroup            Sort a GRangesList
startCodons             Get the Start codons(3 bases) from a
                        GRangesList of orfs grouped by orfs
startDefinition         Returns start definitions
startRegionString       Get -20,20 start region as DNA characters per
                        gr group
startSites              Get the start sites from a GRangesList of orfs
                        grouped by orfs
stopCodons              Get the Stop codons (3 bases) from a
                        GRangesList of orfs grouped by orfs
stopDefinition          Returns stop definitions
stopSites               Get the stop sites from a GRangesList of orfs
                        grouped by orfs
strandBool              Get logical list of strands
strandPerGroup          Get list of strands per granges group
subsetCoverage          Subset GRanges to get coverage.
subset_to_frame         Subset GRanges to get desired frame. GRanges
                        object should be beforehand tiled to size of 1.
                        This subsetting takes account for strand.
tile1                   Tile a GRangesList by 1
translationalEff        Translational efficiency
txLen                   Get transcript lengths
txNames                 Get transcript names from orf names
txNamesWithLeaders      Get the transcripts that have minimum lengths
                        of leaders and cds.
txSeqsFromFa            Get transcript sequence from a GrangesList and
                        a faFile or BSgenome
uORFSearchSpace         Create search space to look for uORFs
uniqueGroups            Get the unique set of groups in a GRangesList
uniqueOrder             Get unique ordering for GRangesList groups
unlistGrl               Safe unlist
updateTxdbRanks         Update exon ranks of exon data.frame
updateTxdbStartSites    Update start sites of leaders
upstreamFromPerGroup    Get rest of objects upstream (inclusive)
upstreamOfPerGroup      Get rest of objects upstream (exclusive)
validGRL                Helper Function to check valid GRangesList
                        input
widthPerGroup           Get list of widths per granges group
windowPerGroup          Get window region of tx around point of gr
