A B C D E F G H I K L M N O P Q R S T U W
ORFik-package | ORFik for analysis of open reading frames. |
artificial.orfs | Create small artificial orfs from cds |
assignTSSByCage | Input a txdb and add a 5' leader for each transcript, that does not have one. |
asTX | Map genomic to transcript coordinates by reference |
bamVarName | Get library variable names from ORFik 'experiment' |
codon_usage | Codon usage |
codon_usage_exp | Codon analysis for ORFik experiment |
codon_usage_plot | Plot codon_usage |
collapse.fastq | Very fast fastq/fasta collapser |
collapseDuplicatedReads | Collapse duplicated reads |
collapseDuplicatedReads-method | Collapse duplicated reads |
collapseDuplicatedReads-method | Collapse duplicated reads |
collapseDuplicatedReads-method | Collapse duplicated reads |
collapseDuplicatedReads-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 |
correlation.plots | Correlation plots between all samples |
cor_plot | Get correlation between columns |
cor_table | Get correlation between columns |
countOverlapsW | CountOverlaps with weights |
countTable | Extract count table directly from experiment |
countTable_regions | Make a list of count matrices from experiment |
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 |
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 |
create.experiment | Create an ORFik 'experiment' |
defineTrailer | Defines trailers for ORF. |
DEG.analysis | Run differential TE analysis |
DEG.plot.static | Plot DEG result |
DEG_model | Get DESeq2 model without running results |
DEG_model_results | Get DESeq2 model results from model |
design-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 |
DTEG.analysis | Run differential TE analysis |
DTEG.plot | Plot DTEG result |
entropy | Percentage of maximum entropy |
envExp | Get ORFik experiment environment |
envExp-method | Get ORFik experiment environment |
envExp<- | Set ORFik experiment environment |
envExp<--method | Set ORFik experiment environment |
experiment | experiment class definition |
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-method | Store GRanges / GAlignments object as .ofst |
export.ofst-method | Store GRanges / GAlignments object as .ofst |
export.ofst-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-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 |
findUORFs_exp | 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-method | length covRle |
length-method | length covRleList |
lengths-method | lengths covRle |
lengths-method | lengths covRleList |
libFolder | Get ORFik experiment library folder |
libFolder-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 |
metadata.autnaming | Guess SRA metadata columns |
metaWindow | Calculate meta-coverage of reads around input GRanges/List object. |
name | Get name of ORFik experiment |
name-method | Get name of ORFik experiment |
nrow-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 |
ORFik | 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 |
orfScore | Get ORFscore for a GRangesList of ORFs |
organism-method | Get ORFik experiment organism |
outputLibs | Output NGS libraries to R as variables |
pcaExperiment | Simple PCA analysis |
pmapFromTranscriptF | Faster pmapFromTranscript |
pmapToTranscriptF | Faster pmapToTranscript |
pSitePlot | Plot area around TIS as histogram |
QCfolder | Get ORFik experiment QC folder path |
QCfolder-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 |
r | strandMode covRle |
r-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 |
RiboQC.plot | Quality control for pshifted Ribo-seq data |
ribosomeReleaseScore | Ribosome Release Score (RRS) |
ribosomeStallingScore | Ribosome Stalling Score (RSS) |
ribo_fft | Get periodogram data per read length |
ribo_fft_plot | Get periodogram plot per read length |
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-method | Seqinfo covRle Extracted from forward RleList |
seqinfo-method | Seqinfo covRle Extracted from forward RleList |
seqinfo-method | Seqinfo ORFik experiment Extracted from fasta genome index |
seqlevels-method | Seqlevels covRle Extracted from forward RleList |
seqlevels-method | Seqlevels covRleList Extracted from forward RleList |
seqlevels-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-method | covRle show definition |
show-method | covRleList show definition |
show-method | experiment show definition |
simpleLibs | Converted format of NGS libraries |
sortPerGroup | Sort a GRangesList |
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 |
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-method | strandMode covRle |
strandMode-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-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. |
TOP.Motif.ecdf | TOP Motif ecdf plot |
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 |
uniqueGroups | Get the unique set of groups in a GRangesList |
uniqueOrder | Get unique ordering for GRangesList groups |
unlistGrl | Safe unlist |
uORFSearchSpace | Create search space to look for uORFs |
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 |