DEG.analysis            Run differential TE analysis
DEG.plot.static         Plot DEG result
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
ORFik.template.experiment.zf
                        An ORFik experiment to see how it looks
ORFikQC                 A post Alignment quality control of reads
QCfolder                Get ORFik experiment QC folder path
QCfolder,experiment-method
                        Get ORFik experiment QC folder path
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
artificial.orfs         Create small artificial orfs from cds
asTX                    Map genomic to transcript coordinates by
                        reference
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'
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 main features in ORFik
computeFeaturesCage     Get all main features in ORFik
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
convert_bam_to_ofst     Convert libraries to ofst
convert_to_bigWig       Convert to BigWig
convert_to_covRle       Convert libraries to covRle
convert_to_covRleList   Convert libraries to covRleList objects
convert_to_fstWig       Convert to fstwig
cor_plot                Get correlation between columns
cor_table               Get correlation between columns
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
covRle                  Coverage Rlelist for both strands
covRle-class            Coverage Rle for both strands or single
covRleFromGR            Convert GRanges to covRle
covRleList              Coverage Rlelist for both strands
covRleList-class        List of covRle
coverageByTranscriptC   coverageByTranscript with coverage input
coverageByTranscriptW   coverageByTranscript with weights
coverageHeatMap         Create a heatmap of coverage
coveragePerTiling       Get coverage per group
coverageScorings        Add a coverage scoring scheme
coverage_to_dt          Convert coverage RleList to data.table
create.experiment       Create an ORFik 'experiment'
defineTrailer           Defines trailers for ORF.
design,experiment-method
                        Get experimental design Find the column/columns
                        that create a separation between samples, by
                        default skips replicate and choose first that
                        is from either: libtype, condition, stage and
                        fraction.
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
entropy                 Percentage of maximum entropy
envExp                  Get ORFik experiment environment
envExp,experiment-method
                        Get ORFik experiment environment
envExp<-                Set ORFik experiment environment
envExp<-,experiment-method
                        Set ORFik experiment environment
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.bigWig           Export as bigWig format
export.fstwig           Export as fstwig (fastwig) format
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
f                       strandMode covRle
f,covRle-method         strandMode covRle
filepath                Get filepaths to ORFik experiment
filterExtremePeakGenes
                        Filter out transcript by a median filter
filterTranscripts       Filter transcripts by lengths
fimport                 Load any type of sequencing reads
findFa                  Convenience wrapper for Rsamtools FaFile
findMapORFs             Find ORFs and immediately map them to their
                        genomic positions.
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
flankPerGroup           Get flanks per group
floss                   Fragment Length Organization Similarity Score
fpkm                    Create normalizations of overlapping read
                        counts.
fractionLength          Fraction Length
fread.bed               Load bed file as GRanges
gcContent               Get GC content
geneToSymbol            Get gene symbols from Ensembl gene ids
getGenomeAndAnnotation
                        Download genome (fasta), annotation (GTF) and
                        contaminants
get_bioproject_candidates
                        Query eutils for bioproject IDs
get_silva_rRNA          Download Silva SSU & LSU sequences
groupGRangesBy          Group GRanges
groupings               Get number of ranges per group as an iteration
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.fstwig           Import region from fastwig
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
isInFrame               Find frame for each orf relative to cds
isOverlapping           Find frame for each orf relative to cds
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
length,covRle-method    length covRle
length,covRleList-method
                        length covRleList
lengths,covRle-method   lengths covRle
lengths,covRleList-method
                        lengths covRleList
libFolder               Get ORFik experiment library folder
libFolder,experiment-method
                        Get ORFik experiment library folder
libraryTypes            Which type of library type in 'experiment'?
list.experiments        List current experiment available
list.genomes            List genomes created with ORFik
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
makeORFNames            Make ORF names per orf
makeSummarizedExperimentFromBam
                        Make a count matrix from a library or
                        experiment
makeTxdbFromGenome      Make txdb from genome
mergeFastq              Merge groups of Fastq /Fasta files
mergeLibs               Merge and save libraries of experiment
metaWindow              Calculate meta-coverage of reads around input
                        GRanges/List object.
metadata.autnaming      Guess SRA metadata columns
name                    Get name of ORFik experiment
name,experiment-method
                        Get name of ORFik experiment
nrow,experiment-method
                        Internal nrow function for ORFik experiment
                        Number of runs in experiment
numExonsPerGroup        Get list of the number of exons per group
ofst_merge              Merge multiple ofst file
optimizedTranscriptLengths
                        Load length and names of all transcripts
orfFrameDistributions   Find shifted Ribo-seq frame distributions
orfScore                Get ORFscore for a GRangesList of ORFs
organism,experiment-method
                        Get ORFik experiment organism
outputLibs              Output NGS libraries to R as variables
pSitePlot               Plot area around TIS as histogram
pcaExperiment           Simple PCA analysis
pmapFromTranscriptF     Faster pmapFromTranscript
pmapToTranscriptF       Faster pmapToTranscript
r                       strandMode covRle
r,covRle-method         strandMode covRle
rankOrder               ORF rank in transcripts
read.experiment         Read ORFik 'experiment'
readBam                 Custom bam reader
readBigWig              Custom bigWig reader
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
remove.experiments      Remove ORFik experiment libraries load in R
ribo_fft                Get periodogram data per read length
ribo_fft_plot           Get periodogram plot per read length
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
scaledWindowPositions   Scale (bin) windows to a meta window of given
                        size
scoreSummarizedExperiment
                        Helper function for
                        makeSummarizedExperimentFromBam
seqinfo,covRle-method   Seqinfo covRle Extracted from forward RleList
seqinfo,covRleList-method
                        Seqinfo covRle Extracted from forward RleList
seqinfo,experiment-method
                        Seqinfo ORFik experiment Extracted from fasta
                        genome index
seqlevels,covRle-method
                        Seqlevels covRle Extracted from forward RleList
seqlevels,covRleList-method
                        Seqlevels covRleList Extracted from forward
                        RleList
seqlevels,experiment-method
                        Seqlevels ORFik experiment Extracted from fasta
                        genome index
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,covRle-method      covRle show definition
show,covRleList-method
                        covRleList show definition
show,experiment-method
                        experiment show definition
simpleLibs              Converted format of NGS libraries
sortPerGroup            Sort a GRangesList
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
strandMode,covRle-method
                        strandMode covRle
strandMode,covRleList-method
                        strandMode covRle
strandPerGroup          Get list of strands per granges group
subsetToFrame           Subset GRanges to get desired frame.
symbols                 Get ORFik experiment QC folder path
symbols,experiment-method
                        Get ORFik experiment QC folder path
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.
topMotif                TOP Motif detection
transcriptWindow        Make 100 bases size meta window for all
                        libraries in experiment
translationalEff        Translational efficiency
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
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
