Roleren/ORFik
Open Reading Frames in Genomics

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Roleren/ORFik: Open Reading Frames in Genomics
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API

API for Roleren/ORFik
Open Reading Frames in Genomics

Global functions
DEG.analysis Man page Source code
DEG.plot.static Man page Source code
DEG_DESeq Source code
DEG_design Source code
DEG_input_validation Source code
DEG_model Man page Source code
DEG_model_results Man page Source code
DEG_model_simple Man page Source code
DTEG.analysis Man page Source code
DTEG.plot Man page Source code
DTEG_input_validation Source code
DTEG_model_results Source code
ORFik Man page
ORFik-package Man page
ORFik.template.experiment Man page Source code
ORFik.template.experiment.zf Man page Source code
ORFikQC Man page
QC_count_tables Man page Source code
QCfolder Man page
QCfolder,experiment-method Man page
QCplots Man page Source code
QCreport Man page Source code
QCstats Man page Source code
QCstats.plot Man page Source code
RiboQC.plot Man page
SRP_from_GSE Source code
STAR.align.folder Man page Source code
STAR.align.single Man page Source code
STAR.allsteps.multiQC Man page Source code
STAR.index Man page Source code
STAR.install Man page Source code
STAR.multiQC Man page Source code
STAR.multiQC_plot Source code
STAR.remove.crashed.genome Man page Source code
STAR_read_log_files Source code
TOP.Motif.ecdf Man page
abstract_save Source code
addCdsOnLeaderEnds Man page Source code
addNewTSSOnLeaders Man page Source code
add_author Source code
add_file_paths Source code
add_pseudo_5utrs_txdb_if_needed Man page Source code
add_pubmed_id Source code
add_reference_info Source code
alignmentFeatureStatistics Man page Source code
allFeaturesHelper Man page Source code
appendZeroes Man page
artificial.orfs Man page Source code
asTX Man page Source code
assignAnnotations Man page
assignFirstExonsStartSite Man page Source code
assignLastExonsStopSite Man page Source code
assignTSSByCage Man page Source code
auto_detect_gtf_in_dir Source code
bamVarName Man page Source code
bamVarNamePicker Man page Source code
batchNames Man page Source code
bedToGR Man page Source code
browseSRA Man page Source code
categorize_ORFs Source code
categorize_and_filter_ORFs Source code
cellLineNames Man page Source code
cellTypeNames Man page Source code
changePointAnalysis Man page Source code
checkRFP Man page Source code
checkRNA Man page Source code
check_for_na_covRle Source code
check_for_na_coverage Source code
clean_file_extension Source code
codonSumsPerGroup Man page Source code
codon_usage Man page
codon_usage_exp Man page
codon_usage_plot Man page
collapse.by.scores Man page Source code
collapse.fastq Man page Source code
collapse.fastq.internal Source code
collapseDuplicatedReads Man page
collapseDuplicatedReads,GAlignmentPairs-method Man page
collapseDuplicatedReads,GAlignments-method Man page
collapseDuplicatedReads,GRanges-method Man page
collapseDuplicatedReads,data.table-method Man page
combn.pairs Man page
computeFeatures Man page Source code
computeFeaturesCage Man page Source code
conditionNames Man page Source code
config Man page Source code
config.exper Man page Source code
config.save Man page Source code
config_file Man page Source code
contaminants_download Source code
contaminants_processing Source code
convertLibs Man page Source code
convertToOneBasedRanges Man page Source code
convert_bam_to_ofst Man page Source code
convert_to_bigWig Man page Source code
convert_to_covRle Man page Source code
convert_to_covRleList Man page Source code
convert_to_fstWig Man page Source code
cor_plot Man page
cor_table Man page
correlation.plots Man page
countOverlapsW Man page Source code
countTable Man page Source code
countTable_regions Man page Source code
covRle Man page Source code
covRle-class Man page
covRleFromGR Man page Source code
covRleList Man page Source code
covRleList-class Man page
coverageByTranscriptC Man page
coverageByTranscriptW Man page
coverageGroupings Man page
coverageHeatMap Man page Source code
coveragePerORFStatistics Source code
coveragePerTiling Man page
coverageScorings Man page
coverage_to_dt Man page
create.experiment Man page Source code
defineIsoform Man page
defineTrailer Man page Source code
design,experiment-method Man page
detectRibosomeShifts Man page Source code
detect_ribo_orfs Man page
disengagementScore Man page
distToCds Man page Source code
distToTSS Man page Source code
download.SRA Man page Source code
download.SRA.metadata Man page Source code
download.ebi Man page Source code
downstreamFromPerGroup Man page Source code
downstreamN Man page Source code
downstreamOfPerGroup Man page Source code
entropy Man page Source code
envExp Man page
envExp,experiment-method Man page
envExp<- Man page
envExp<-,experiment-method Man page
exists.ftp.dir.fast Man page
exists.ftp.file.fast Man page
experiment Man page
experiment-class Man page
experiment.colors Man page Source code
experiment_parse_list_info Source code
export.bed12 Man page Source code
export.bedo Man page Source code
export.bedoc Man page Source code
export.bigWig Man page Source code
export.cov Source code
export.covlist Source code
export.fstwig Man page Source code
export.ofst Man page
export.ofst,GAlignmentPairs-method Man page
export.ofst,GAlignments-method Man page
export.ofst,GRanges-method Man page
export.wiggle Man page Source code
extendLeaders Man page Source code
extendTrailers Man page Source code
extendsTSSexons Man page Source code
extract_run_id Man page Source code
f Man page
f,covRle-method Man page
fetch_xml_attributes Source code
filepath Man page Source code
filepath_errors Source code
filterCage Man page Source code
filterExtremePeakGenes Man page Source code
filterTranscripts Man page
filterUORFs Man page Source code
filter_empty_runs Source code
fimport Man page Source code
findFa Man page Source code
findFromPath Man page Source code
findLibrariesInFolder Man page Source code
findMapORFs Man page Source code
findMaxPeaks Man page Source code
findNGSPairs Man page Source code
findNewTSS Man page Source code
findORFs Man page Source code
findORFsFasta Man page Source code
findORFs_fasta Source code
findPeaksPerGene Man page
findUORFs Man page Source code
findUORFs_exp Man page Source code
find_pairs_from_folder Source code
find_url_ebi Man page Source code
find_url_ebi_safe Man page Source code
firstEndPerGroup Man page Source code
firstExonPerGroup Man page Source code
firstStartPerGroup Man page Source code
fix_malformed_gff Man page Source code
flankPerGroup Man page Source code
floss Man page
footprints.analysis Man page Source code
format_file_pairs_result Source code
fpkm Man page Source code
fpkm_calc Man page Source code
fractionLength Man page Source code
fractionNames Man page Source code
fread.bed Man page Source code
gSort Man page Source code
gcContent Man page Source code
geneToSymbol Man page
getGAlignments Man page Source code
getGAlignmentsPairs Man page Source code
getGRanges Man page Source code
getGenomeAndAnnotation Man page Source code
getGtfPathFromTxdb Man page
getNGenesCoverage Man page
getWeights Man page Source code
get_bioproject_candidates Man page Source code
get_genome_fasta Man page Source code
get_genome_gtf Man page Source code
get_noncoding_rna Man page Source code
get_phix_genome Man page Source code
get_rRNA Source code
get_silva_rRNA Man page Source code
get_tRNA Source code
groupGRangesBy Man page Source code
groupings Man page
guess_metadata_from_filepaths Source code
hasHits Man page Source code
heatMapL Man page Source code
heatMapRegion Man page Source code
heatMap_single Man page Source code
import.bedo Man page Source code
import.bedoc Man page Source code
import.fstwig Man page Source code
import.ofst Man page Source code
importGtfFromTxdb Man page
inhibitorNames Man page Source code
initiationScore Man page
insideOutsideORF Man page
install.fastp Man page Source code
install.sratoolkit Man page Source code
is.ORF Man page Source code
is.gr_or_grl Man page Source code
is.grl Man page Source code
is.range Man page Source code
isInFrame Man page Source code
isOverlapping Man page Source code
isPeriodic Man page Source code
kozakHeatmap Man page Source code
kozakSequenceScore Man page Source code
kozak_IR_ranking Man page
lastExonEndPerGroup Man page Source code
lastExonPerGroup Man page Source code
lastExonStartPerGroup Man page Source code
length,covRle-method Man page
length,covRleList-method Man page
lengths,covRle-method Man page
lengths,covRleList-method Man page
libFolder Man page
libFolder,experiment-method Man page
libNames Man page Source code
libraryTypes Man page Source code
libs_are_loaded Source code
list.experiments Man page Source code
list.genomes Man page Source code
loadRegion Man page
loadRegions Man page
loadTranscriptType Man page
loadTxdb Man page
longestORFs Man page Source code
mainNames Man page Source code
makeExonRanks Man page Source code
makeORFNames Man page Source code
makeSummarizedExperimentFromBam Man page Source code
makeTxdbFromGenome Man page Source code
mapToGRanges Man page Source code
matchColors Man page Source code
matchNaming Man page Source code
matchSeqStyle Man page
mergeFastq Man page Source code
mergeLibs Man page Source code
metaWindow Man page Source code
metadata.autnaming Man page Source code
metadata_count_table Source code
model.matrix,experiment-method Man page
name Man page
name,experiment-method Man page
name_decider Source code
nrow,experiment-method Man page
numCodons Man page
numExonsPerGroup Man page Source code
ofst_merge Man page
optimizeReads Man page
optimizedTranscriptLengths Man page
optimized_txdb_path Man page
orfFrameDistributions Man page Source code
orfID Man page Source code
orfScore Man page
orfs_as_IRanges Source code
orfs_as_List Source code
organism,experiment-method Man page
outputLibs Man page Source code
pSitePlot Man page Source code
pasteDir Man page Source code
pcaExperiment Man page
percentage_to_ratio Man page Source code
plotHelper Man page Source code
pmapFromTranscriptF Man page Source code
pmapFromTranscriptsCPP Source code
pmapToTranscriptF Man page Source code
pmapToTranscriptsCPP Source code
prettyScoring Man page Source code
pseudo.transform Man page
pshifts_export Source code
r Man page
r,covRle-method Man page
rankOrder Man page Source code
read.experiment Man page Source code
readBam Man page Source code
readBigWig Man page Source code
readLengthTable Man page Source code
readWidths Man page Source code
readWig Man page Source code
reassignTSSbyCage Man page Source code
reassignTxDbByCage Man page Source code
reduceKeepAttr Man page Source code
regionPerReadLength Man page
remakeTxdbExonIds Man page Source code
remove.experiments Man page Source code
remove.file_ext Man page
removeMetaCols Man page
removeORFsWithSameStartAsCDS Man page Source code
removeORFsWithSameStopAsCDS Man page Source code
removeORFsWithStartInsideCDS Man page Source code
removeORFsWithinCDS Man page Source code
removeTxdbExons Man page
removeTxdbTranscripts Man page
rename.SRA.files Man page Source code
repNames Man page Source code
resFolder Man page
resFolder,experiment-method Man page
restrictTSSByUpstreamLeader Man page Source code
revElementsF Man page
reverseMinusStrandPerGroup Man page Source code
riboORFs Man page
riboORFsFolder Man page
ribo_fft Man page Source code
ribo_fft_plot Man page Source code
ribosomeReleaseScore Man page
ribosomeStallingScore Man page
rnaNormalize Man page Source code
runIDs Man page
runIDs,experiment-method Man page
sample_info_download Source code
sample_info_single Source code
save.experiment Man page Source code
save.fstwig Source code
savePlot Man page Source code
scaledWindowPositions Man page Source code
scoreSummarizedExperiment Man page Source code
seq_usage Source code
seqinfo,covRle-method Man page
seqinfo,covRleList-method Man page
seqinfo,experiment-method Man page
seqlevels,covRle-method Man page
seqlevels,covRleList-method Man page
seqlevels,experiment-method Man page
seqnamesPerGroup Man page Source code
shiftFootprints Man page Source code
shiftFootprintsByExperiment Man page
shiftPlots Man page
shift_narrow Source code
shifts.load Man page
shifts_load Man page Source code
shifts_save Man page Source code
show,covRle-method Man page
show,covRleList-method Man page
show,experiment-method Man page
simpleLibs Man page
sortPerGroup Man page Source code
splitIn3Tx Man page Source code
stageNames Man page Source code
startCodons Man page Source code
startDefinition Man page Source code
startRegion Man page Source code
startRegionCoverage Man page
startRegionString Man page Source code
startSites Man page Source code
stopCodons Man page Source code
stopDefinition Man page Source code
stopRegion Man page Source code
stopSites Man page Source code
strandBool Man page Source code
strandMode,covRle-method Man page
strandMode,covRleList-method Man page
strandPerGroup Man page Source code
study_runinfo_download_deprecated Source code
subsetCoverage Man page Source code
subsetToFrame Man page Source code
subset_count_table Source code
sum,covRle-method Man page
symbols Man page
symbols,experiment-method Man page
te.plot Man page Source code
te.table Man page Source code
te_rna.plot Man page Source code
tile1 Man page Source code
tissueNames Man page Source code
topMotif Man page Source code
transcriptWindow Man page Source code
transcriptWindow1 Man page Source code
transcriptWindowPer Man page Source code
translationalEff Man page
trim_detection Man page
trim_detection_message Source code
trimming.table Man page Source code
txNames Man page Source code
txNamesToGeneNames Man page
txSeqsFromFa Man page Source code
uORFSearchSpace Man page Source code
uniqueGroups Man page Source code
uniqueOrder Man page Source code
unlistGrl Man page
updateTxdbRanks Man page
updateTxdbStartSites Man page
upstreamFromPerGroup Man page Source code
upstreamOfPerGroup Man page Source code
validGRL Man page Source code
validSeqlevels Man page Source code
validateExperiments Man page Source code
widthPerGroup Man page Source code
windowCoveragePlot Man page Source code
windowPerGroup Man page Source code
windowPerReadLength Man page
windowPerTranscript Man page Source code
xAxisScaler Man page Source code
yAxisScaler Man page Source code
Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.

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