DTEG.analysis           Run differential TE analysis
DTEG.plot               Plot DTEG result
ORFik-package           ORFik for analysis of open reading frames.
ORFik.template.experiment
                        An ORFik experiment to see how it looks
ORFikQC                 A post Alignment quality control of reads
QC_count_tables         Create count table info for QC report
QCplots                 Correlation and coverage plots for ORFikQC
QCreport                A post Alignment quality control of reads
QCstats                 Load ORFik QC Statistics report
QCstats.plot            Make plot of ORFik QCreport
RiboQC.plot             Quality control for pshifted Ribo-seq data
STAR.align.folder       Align all libraries in folder with STAR
STAR.align.single       Align single or paired end pair with STAR
STAR.allsteps.multiQC   Create STAR multiQC plot and table
STAR.index              Create STAR genome index
STAR.install            Download and prepare STAR
STAR.multiQC            Create STAR multiQC plot and table
STAR.remove.crashed.genome
                        Remove crashed STAR genome
TOP.Motif.ecdf          TOP Motif ecdf plot
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.
allFeaturesHelper       Calculate the features in computeFeatures
                        function
artificial.orfs         Create small artificial orfs from cds
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.
bamVarName              Get library variable names from ORFik
                        'experiment'
bamVarNamePicker        Get variable name per filepath in experiment
bedToGR                 Converts bed style data.frame to Granges
cellLineNames           Get cell-line name variants
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 read hits per codon
collapse.by.scores      Merge reads by sum of existing scores
collapse.fastq          Very fast fastq/fasta collapser
collapseDuplicatedReads
                        Collapse duplicated reads
collapseDuplicatedReads,GAlignmentPairs-method
                        Collapse duplicated reads
collapseDuplicatedReads,GAlignments-method
                        Collapse duplicated reads
collapseDuplicatedReads,GRanges-method
                        Collapse duplicated reads
combn.pairs             Create all unique combinations pairs possible
computeFeatures         Get all possible features in ORFik
computeFeaturesCage     Get all possible features in ORFik
conditionNames          Get condition name variants
config                  Read directory config for ORFik experiments
config.exper            Set directories for experiment
config.save             Save/update directory config for ORFik
                        experiments
convertLibs             Converted format of NGS libraries
convertToOneBasedRanges
                        Convert a GRanges Object to 1 width reads
correlation.plots       Correlation plots between all samples
countOverlapsW          CountOverlaps with weights
countTable              Extract count table directly from experiment
countTable_regions      Make a list of count matrices from experiment
coverageByTranscriptW   coverageByTranscript with weights
coverageGroupings       Get grouping for a coverage table in ORFik
coverageHeatMap         Create a heatmap of coverage
coveragePerTiling       Get coverage per group
coverageScorings        Add a coverage scoring scheme
create.experiment       Create a ORFik 'experiment'
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
download.SRA            Download read libraries from SRA
download.SRA.metadata   Downloads metadata from SRA
download.ebi            Faster download of fastq files
downstreamFromPerGroup
                        Get rest of objects downstream (inclusive)
downstreamN             Restrict GRangesList
downstreamOfPerGroup    Get rest of objects downstream (exclusive)
entropy                 Percentage of maximum entropy
exists.ftp.file.fast    A copy of biomartr ftp check
experiment-class        experiment class definition
experiment.colors       Decide color for libraries by grouping
export.bed12            Export as bed12 format
export.bedo             Store GRanges object as .bedo
export.bedoc            Store GAlignments object as .bedoc
export.ofst             Store GRanges / GAlignments object as .ofst
export.ofst,GAlignmentPairs-method
                        Store GRanges / GAlignments object as .ofst
export.ofst,GAlignments-method
                        Store GRanges / GAlignments object as .ofst
export.ofst,GRanges-method
                        Store GRanges / GAlignments object as .ofst
export.wiggle           Export as wiggle format
extendLeaders           Extend the leaders transcription start sites.
extendTrailers          Extend the Trailers transcription stop sites
extendsTSSexons         Extend first exon of each transcript with
                        length specified
filepath                Get filepaths to ORFik experiment
filterCage              Filter peak of cage-data by value
filterExtremePeakGenes
                        Filter out transcript by a median filter
filterTranscripts       Filter transcripts by lengths
filterUORFs             Remove uORFs that are false CDS hits
fimport                 Load any type of sequencing reads
findFa                  Convenience wrapper for Rsamtools FaFile
findFromPath            Find all candidate library types filenames
findLibrariesInFolder   Get all library files in folder/folders of
                        given types
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
findNGSPairs            Find pair of forward and reverse strand wig /
                        bed files and paired end bam files split in two
findNewTSS              Finds max peaks per trancsript from reads in
                        the cagefile
findORFs                Find Open Reading Frames.
findORFsFasta           Finds Open Reading Frames in fasta files.
findPeaksPerGene        Find peaks per gene
findUORFs               Find upstream ORFs from transcript annotation
find_url_ebi            Locates and check if fastq files exists in ebi
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
footprints.analysis     Pre shifting plot analysis
fpkm                    Create normalizations of overlapping read
                        counts.
fpkm_calc               Create normalizations of read counts
fractionLength          Fraction Length
fread.bed               Load bed file as GRanges
gSort                   Sort a GRangesList, helper.
gcContent               Get GC content
getGAlignments          Internal GAlignments loader from fst data.frame
getGAlignmentsPairs     Internal GAlignmentPairs loader from fst
                        data.frame
getGRanges              Internal GRanges loader from fst data.frame
getGenomeAndAnnotation
                        Download genome (fasta), annotation (GTF) and
                        contaminants
getNGenesCoverage       Get number of genes per coverage table
getWeights              Get weights from a subject GenomicRanges object
get_genome_fasta        Download genome (fasta), annotation (GTF) and
                        contaminants
get_genome_gtf          Download genome (fasta), annotation (GTF) and
                        contaminants
get_noncoding_rna       Download genome (fasta), annotation (GTF) and
                        contaminants
get_phix_genome         Download genome (fasta), annotation (GTF) and
                        contaminants
get_silva_rRNA          Download Silva SSU & LSU sequences
groupGRangesBy          Group GRanges
groupings               Get number of ranges per group as an iteration
hasHits                 Hits from reads
heatMapL                Coverage heatmap of multiple libraries
heatMapRegion           Create coverage heatmaps of specified region
heatMap_single          Coverage heatmap of single libraries
import.bedo             Load GRanges object from .bedo
import.bedoc            Load GAlignments object from .bedoc
import.ofst             Load GRanges / GAlignments object from .ofst
importGtfFromTxdb       Import the GTF / GFF that made the txdb
initiationScore         Get initiation score for a GRangesList of ORFs
insideOutsideORF        Inside/Outside score (IO)
install.fastp           Download and prepare fastp trimmer
install.sratoolkit      Download sra toolkit
is.ORF                  Check if all requirements for an ORFik ORF is
                        accepted.
is.gr_or_grl            Helper function to check for GRangesList or
                        GRanges class
is.grl                  Helper function to check for GRangesList
is.range                Helper function to check for ranged object
isInFrame               Find frame for each orf relative to cds
isOverlapping           Find frame for each orf relative to cds
isPeriodic              Find if there is a periodicity of 3 in the
                        vector
kozakHeatmap            Make sequence region heatmap relative to
                        scoring
kozakSequenceScore      Make a score for each ORFs start region by
                        proximity to Kozak
kozak_IR_ranking        Rank kozak initiation sequences
lastExonEndPerGroup     Get last end per granges group
lastExonPerGroup        Get last exon per GRangesList group
lastExonStartPerGroup   Get last start per granges group
libNames                Get library name variants
libraryTypes            Which type of library type in 'experiment'?
list.experiments        List current experiment available
loadRegion              Load transcript region
loadRegions             Get all regions of transcripts specified to
                        environment
loadTranscriptType      Load transcripts of given biotype
loadTxdb                General loader for txdb
longestORFs             Get longest ORF per stop site
mainNames               Get main name from variant name
makeExonRanks           Make grouping by exons ranks
makeORFNames            Make ORF names per orf
makeSummarizedExperimentFromBam
                        Make a count matrix from a library or
                        experiment
mapToGRanges            Map orfs to genomic coordinates
matchColors             Match coloring of coverage plot
matchNaming             Match naming of GRangesList
matchSeqStyle           A wrapper for seqlevelsStyle
mergeFastq              Merge groups of Fastq /Fasta files
metaWindow              Calculate meta-coverage of reads around input
                        GRanges/List object.
nrow,experiment-method
                        Internal nrow function for ORFik experiment
                        Number of runs in experiment
numCodons               Get number of codons
numExonsPerGroup        Get list of the number of exons per group
optimizeReads           Find optimized subset of valid reads
orfID                   Get id's for each orf
orfScore                Get ORFscore for a GRangesList of ORFs
organism.df             Get organism of the ORFik experiment
outputLibs              Output bam/bed/bedo/bedoc/ofst/wig files to R
                        as variables
pSitePlot               Plot area around TIS as histogram
pasteDir                A paste function for directories Makes sure
                        slashes are corrected, and not doubled.
percentage_to_ratio     Convert percentage to ratio of 1
plotHelper              Helper function for coverage plots
pmapFromTranscriptF     Faster pmapFromTranscript
pmapToTranscriptF       Faster pmapToTranscript
prettyScoring           Prettify scoring name
pseudo.transform        Transform object
rankOrder               ORF rank in transcripts
read.experiment         Read ORFik 'experiment'
readBam                 Custom bam reader
readLengthTable         Make table of readlengths
readWidths              Get read widths
readWig                 Custom wig reader
reassignTSSbyCage       Reassign all Transcript Start Sites (TSS)
reassignTxDbByCage      Input a txdb and reassign the TSS for each
                        transcript by CAGE
reduceKeepAttr          Reduce GRanges / GRangesList
regionPerReadLength     Find proportion of reads per position per read
                        length in region
remakeTxdbExonIds       Get new exon ids after update of txdb
remove.experiments      Remove bam/bed/wig files load in R as variables
remove.file_ext         Remove file extension of path
removeMetaCols          Removes meta columns
removeORFsWithSameStartAsCDS
                        Remove ORFs that have same start site as the
                        CDS
removeORFsWithSameStopAsCDS
                        Remove ORFs that have same stop site as the CDS
removeORFsWithStartInsideCDS
                        Remove ORFs that have start site within the CDS
removeORFsWithinCDS     Remove ORFs that are within cds
removeTxdbExons         Remove exons in txList that are not in fiveUTRs
removeTxdbTranscripts   Remove specific transcripts in txdb List
rename.SRA.files        Rename SRA files from metadata
repNames                Get replicate name variants
restrictTSSByUpstreamLeader
                        Restrict extension of 5' UTRs to closest
                        upstream leader end
reverseMinusStrandPerGroup
                        Reverse minus strand
ribosomeReleaseScore    Ribosome Release Score (RRS)
ribosomeStallingScore   Ribosome Stalling Score (RSS)
rnaNormalize            Normalize a data.table of coverage by RNA seq
                        per position
save.experiment         Save 'experiment' to disc
savePlot                Helper function for writing plots to disc
scaledWindowPositions   Scale (bin) windows to a meta window of given
                        size
scoreSummarizedExperiment
                        Helper function for
                        makeSummarizedExperimentFromBam
seqnamesPerGroup        Get list of seqnames per granges group
shiftFootprints         Shift footprints by selected offsets
shiftFootprintsByExperiment
                        Shift footprints of each file in experiment
shiftPlots              Plot shifted heatmaps per library
shifts.load             Load the shifts from experiment
show,experiment-method
                        experiment show definition
simpleLibs              Converted format of NGS libraries
sortPerGroup            Sort a GRangesList
splitIn3Tx              Create binned coverage of transcripts, split
                        into the 3 parts.
stageNames              Get stage name variants
startCodons             Get the Start codons(3 bases) from a
                        GRangesList of orfs grouped by orfs
startDefinition         Returns start codon definitions
startRegion             Start region as GRangesList
startRegionCoverage     Start region coverage
startRegionString       Get start region as DNA-strings per GRanges
                        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 codon definitions
stopRegion              Stop region as GRangesList
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.
subsetToFrame           Subset GRanges to get desired frame.
te.plot                 Translational efficiency plots
te.table                Create a TE table
te_rna.plot             Translational efficiency plots
tile1                   Tile each GRangesList group to 1-base
                        resolution.
tissueNames             Get tissue name variants
topMotif                TOP Motif detection
transcriptWindow        Make 100 bases size meta window for all
                        libraries in experiment
transcriptWindow1       Meta coverage over all transcripts
transcriptWindowPer     Helper function for transcriptWindow
translationalEff        Translational efficiency
trim_detection          Add trimming info to QC report
trimming.table          Create trimming table
txNames                 Get transcript names from orf names
txNamesToGeneNames      Convert transcript names to gene names
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 inside
                        txdb object
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
validSeqlevels          Helper function to find overlaping seqlevels
validateExperiments     Validate ORFik 'experiment'
widthPerGroup           Get list of widths per granges group
windowCoveragePlot      Get meta coverage plot of reads
windowPerGroup          Get window region of GRanges object
windowPerReadLength     Find proportion of reads per position per read
                        length in window
windowPerTranscript     Get a binned coverage window per transcript
xAxisScaler             Scale x axis correctly
yAxisScaler             Scale y axis correctly
