Files in JokingHero/ORFik
Open Reading Frames in Genomics
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/Dif_expression_Analysis.R
R/Dif_expression_helpers.R
R/Dif_expression_plots.R
R/ORFik.R
R/ORFs_annotations.R
R/ORFs_helpers.R
R/RcppExports.R
R/RiboORFs_detect_and_classify.R
R/SRA_Entrez_API.R
R/SRA_helper.R
R/SRA_metadata.R
R/STAR.R
R/STAR_multiQC.R
R/SummarizedExperiment_helpers.R
R/cage_annotations.R
R/codon_usage.R
R/compute_Features.R
R/covRLE_class.R
R/coverage_filters.R
R/coverage_heatmaps.R
R/coverage_helpers.R
R/coverage_plots.R
R/experiment.R
R/experiment_IO.R
R/experiment_class.R
R/experiment_naming.R
R/experiment_plots.R
R/fastq_helpers.R
R/feature_helpers.R
R/find_ORFs.R
R/general_plots.R
R/genome_download.R
R/genome_download_helper.R
R/gr_helpers.R
R/gr_or_grl_helpers.R
R/gr_positions.R
R/grl_helpers.R
R/ranges_helpers.R
R/report.R
R/report_helpers.R
R/report_plots.R
R/riboseq_features.R
R/sequence_features.R
R/shift_footprints.R
R/shift_footprints_helpers.R
R/txdbHelpers.R
R/uORF_helpers.R
R/utils.R
R/utils_collapse.R
R/utils_directory_config.R
R/utils_exports.R
R/utils_format_conversion.R
R/utils_imports.R
R/validity.R
README.md
inst/CITATION
inst/STAR_Aligner/RNA_Align_pipeline.sh
inst/STAR_Aligner/RNA_Align_pipeline_folder.sh
inst/STAR_Aligner/STAR_MAKE_INDEX.sh
inst/STAR_Aligner/cleanup_folders.sh
inst/STAR_Aligner/readme.txt
inst/TODO
inst/extdata/Danio_rerio_sample/QC_STATS/countTable_mrna.rds
inst/extdata/Danio_rerio_sample/ofst/ribo-seq.ofst
inst/extdata/Danio_rerio_sample/pshifted/pshifting_arguments.txt
inst/extdata/Danio_rerio_sample/pshifted/ribo-seq_pshifted.ofst
inst/extdata/Danio_rerio_sample/pshifted/ribo-seq_pshifted_forward.wig
inst/extdata/Danio_rerio_sample/pshifted/ribo-seq_pshifted_reverse.wig
inst/extdata/Danio_rerio_sample/pshifted/shifting_table.rds
inst/extdata/Danio_rerio_sample/ribo-seq.bam
inst/extdata/Danio_rerio_sample/ribo-seq.bam.bai
inst/extdata/Homo_sapiens_sample/CAGE_Mutant_rep1.ofst
inst/extdata/Homo_sapiens_sample/CAGE_Mutant_rep2.ofst
inst/extdata/Homo_sapiens_sample/CAGE_WT_rep1.ofst
inst/extdata/Homo_sapiens_sample/CAGE_WT_rep2.ofst
inst/extdata/Homo_sapiens_sample/PAS_Mutant_rep1.ofst
inst/extdata/Homo_sapiens_sample/PAS_Mutant_rep2.ofst
inst/extdata/Homo_sapiens_sample/PAS_WT_rep1.ofst
inst/extdata/Homo_sapiens_sample/PAS_WT_rep2.ofst
inst/extdata/Homo_sapiens_sample/QC_STATS/DTEG_plot.pdf
inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_cds.rds
inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_leaders.rds
inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_mrna.rds
inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_trailers.rds
inst/extdata/Homo_sapiens_sample/RFP_Mutant_rep1.ofst
inst/extdata/Homo_sapiens_sample/RFP_Mutant_rep2.ofst
inst/extdata/Homo_sapiens_sample/RFP_WT_rep1.ofst
inst/extdata/Homo_sapiens_sample/RFP_WT_rep2.ofst
inst/extdata/Homo_sapiens_sample/RNA_Mutant_rep1.ofst
inst/extdata/Homo_sapiens_sample/RNA_Mutant_rep2.ofst
inst/extdata/Homo_sapiens_sample/RNA_WT_rep1.ofst
inst/extdata/Homo_sapiens_sample/RNA_WT_rep2.ofst
inst/extdata/Homo_sapiens_sample/ofst/RFP_Mutant_rep1.ofst
inst/extdata/cage-seq-heart.bed.bgz
inst/extdata/features.rdata
inst/extdata/references/danio_rerio/annotations.gtf
inst/extdata/references/danio_rerio/genome_dummy.fasta
inst/extdata/references/danio_rerio/genome_dummy.fasta.fai
inst/extdata/references/homo_sapiens/Homo_sapiens_dummy.fasta
inst/extdata/references/homo_sapiens/Homo_sapiens_dummy.fasta.fai
inst/extdata/references/homo_sapiens/Homo_sapiens_dummy.gtf
inst/extdata/references/homo_sapiens/Homo_sapiens_dummy.gtf.db
inst/extdata/ribo-seq-heart.bed.bgz
inst/extdata/rna-seq-heart.bed.bgz
inst/images/ORFik_map.png
inst/images/pshift_bazzini.png
man/DEG.analysis.Rd
man/DEG.plot.static.Rd
man/DEG_model.Rd
man/DEG_model_results.Rd
man/DEG_model_simple.Rd
man/DTEG.analysis.Rd
man/DTEG.plot.Rd
man/ORFik-package.Rd
man/ORFik.template.experiment.Rd
man/ORFik.template.experiment.zf.Rd
man/ORFikQC.Rd
man/QC_count_tables.Rd
man/QCfolder-experiment-method.Rd
man/QCfolder.Rd
man/QCplots.Rd
man/QCreport.Rd
man/QCstats.Rd
man/QCstats.plot.Rd
man/RiboQC.plot.Rd
man/STAR.align.folder.Rd
man/STAR.align.single.Rd
man/STAR.allsteps.multiQC.Rd
man/STAR.index.Rd
man/STAR.install.Rd
man/STAR.multiQC.Rd
man/STAR.remove.crashed.genome.Rd
man/TOP.Motif.ecdf.Rd
man/addCdsOnLeaderEnds.Rd
man/addNewTSSOnLeaders.Rd
man/alignmentFeatureStatistics.Rd
man/allFeaturesHelper.Rd
man/appendZeroes.Rd
man/artificial.orfs.Rd
man/asTX.Rd
man/assignAnnotations.Rd
man/assignFirstExonsStartSite.Rd
man/assignLastExonsStopSite.Rd
man/assignTSSByCage.Rd
man/bamVarName.Rd
man/bamVarNamePicker.Rd
man/batchNames.Rd
man/bedToGR.Rd
man/browseSRA.Rd
man/cellLineNames.Rd
man/cellTypeNames.Rd
man/changePointAnalysis.Rd
man/checkRFP.Rd
man/checkRNA.Rd
man/codonSumsPerGroup.Rd
man/codon_usage.Rd
man/codon_usage_exp.Rd
man/codon_usage_plot.Rd
man/collapse.by.scores.Rd
man/collapse.fastq.Rd
man/collapseDuplicatedReads-GAlignmentPairs-method.Rd
man/collapseDuplicatedReads-GAlignments-method.Rd
man/collapseDuplicatedReads-GRanges-method.Rd
man/collapseDuplicatedReads-data.table-method.Rd
man/collapseDuplicatedReads.Rd
man/combn.pairs.Rd
man/computeFeatures.Rd
man/computeFeaturesCage.Rd
man/conditionNames.Rd
man/config.Rd
man/config.exper.Rd
man/config.save.Rd
man/config_file.Rd
man/convertLibs.Rd
man/convertToOneBasedRanges.Rd
man/convert_bam_to_ofst.Rd
man/convert_to_bigWig.Rd
man/convert_to_covRle.Rd
man/convert_to_covRleList.Rd
man/convert_to_fstWig.Rd
man/cor_plot.Rd
man/cor_table.Rd
man/correlation.plots.Rd
man/countOverlapsW.Rd
man/countTable.Rd
man/countTable_regions.Rd
man/covRle-class.Rd
man/covRle.Rd
man/covRleFromGR.Rd
man/covRleList-class.Rd
man/covRleList.Rd
man/coverageByTranscriptC.Rd
man/coverageByTranscriptW.Rd
man/coverageGroupings.Rd
man/coverageHeatMap.Rd
man/coveragePerTiling.Rd
man/coverageScorings.Rd
man/coverage_to_dt.Rd
man/create.experiment.Rd
man/defineIsoform.Rd
man/defineTrailer.Rd
man/design-experiment-method.Rd
man/detectRibosomeShifts.Rd
man/detect_ribo_orfs.Rd
man/disengagementScore.Rd
man/distToCds.Rd
man/distToTSS.Rd
man/download.SRA.Rd
man/download.SRA.metadata.Rd
man/download.ebi.Rd
man/downstreamFromPerGroup.Rd
man/downstreamN.Rd
man/downstreamOfPerGroup.Rd
man/entropy.Rd
man/envExp-experiment-method.Rd
man/envExp-set-experiment-method.Rd
man/envExp-set.Rd
man/envExp.Rd
man/exists.ftp.dir.fast.Rd
man/exists.ftp.file.fast.Rd
man/experiment-class.Rd
man/experiment.colors.Rd
man/export.bed12.Rd
man/export.bedo.Rd
man/export.bedoc.Rd
man/export.bigWig.Rd
man/export.fstwig.Rd
man/export.ofst-GAlignmentPairs-method.Rd
man/export.ofst-GAlignments-method.Rd
man/export.ofst-GRanges-method.Rd
man/export.ofst.Rd
man/export.wiggle.Rd
man/extendLeaders.Rd
man/extendTrailers.Rd
man/extendsTSSexons.Rd
man/extract_run_id.Rd
man/f-covRle-method.Rd
man/f.Rd
man/filepath.Rd
man/filterCage.Rd
man/filterExtremePeakGenes.Rd
man/filterTranscripts.Rd
man/filterUORFs.Rd
man/fimport.Rd
man/findFa.Rd
man/findFromPath.Rd
man/findLibrariesInFolder.Rd
man/findMapORFs.Rd
man/findMaxPeaks.Rd
man/findNGSPairs.Rd
man/findNewTSS.Rd
man/findORFs.Rd
man/findORFsFasta.Rd
man/findPeaksPerGene.Rd
man/findUORFs.Rd
man/findUORFs_exp.Rd
man/find_url_ebi.Rd
man/find_url_ebi_safe.Rd
man/firstEndPerGroup.Rd
man/firstExonPerGroup.Rd
man/firstStartPerGroup.Rd
man/fix_malformed_gff.Rd
man/flankPerGroup.Rd
man/floss.Rd
man/footprints.analysis.Rd
man/fpkm.Rd
man/fpkm_calc.Rd
man/fractionLength.Rd
man/fractionNames.Rd
man/fread.bed.Rd
man/gSort.Rd
man/gcContent.Rd
man/geneToSymbol.Rd
man/getGAlignments.Rd
man/getGAlignmentsPairs.Rd
man/getGRanges.Rd
man/getGenomeAndAnnotation.Rd
man/getGtfPathFromTxdb.Rd
man/getNGenesCoverage.Rd
man/getWeights.Rd
man/get_bioproject_candidates.Rd
man/get_genome_fasta.Rd
man/get_genome_gtf.Rd
man/get_noncoding_rna.Rd
man/get_phix_genome.Rd
man/get_silva_rRNA.Rd
man/groupGRangesBy.Rd
man/groupings.Rd
man/hasHits.Rd
man/heatMapL.Rd
man/heatMapRegion.Rd
man/heatMap_single.Rd
man/import.bedo.Rd
man/import.bedoc.Rd
man/import.fstwig.Rd
man/import.ofst.Rd
man/importGtfFromTxdb.Rd
man/inhibitorNames.Rd
man/initiationScore.Rd
man/insideOutsideORF.Rd
man/install.fastp.Rd
man/install.sratoolkit.Rd
man/is.ORF.Rd
man/is.gr_or_grl.Rd
man/is.grl.Rd
man/is.range.Rd
man/isInFrame.Rd
man/isOverlapping.Rd
man/isPeriodic.Rd
man/kozakHeatmap.Rd
man/kozakSequenceScore.Rd
man/kozak_IR_ranking.Rd
man/lastExonEndPerGroup.Rd
man/lastExonPerGroup.Rd
man/lastExonStartPerGroup.Rd
man/length-covRle-method.Rd
man/length-covRleList-method.Rd
man/lengths-covRle-method.Rd
man/lengths-covRleList-method.Rd
man/libFolder-experiment-method.Rd
man/libFolder.Rd
man/libNames.Rd
man/libraryTypes.Rd
man/list.experiments.Rd
man/list.genomes.Rd
man/loadRegion.Rd
man/loadRegions.Rd
man/loadTranscriptType.Rd
man/loadTxdb.Rd
man/longestORFs.Rd
man/mainNames.Rd
man/makeExonRanks.Rd
man/makeORFNames.Rd
man/makeSummarizedExperimentFromBam.Rd
man/makeTxdbFromGenome.Rd
man/mapToGRanges.Rd
man/matchColors.Rd
man/matchNaming.Rd
man/matchSeqStyle.Rd
man/mergeFastq.Rd
man/mergeLibs.Rd
man/metaWindow.Rd
man/metadata.autnaming.Rd
man/model.matrix-experiment-method.Rd
man/name-experiment-method.Rd
man/name.Rd
man/nrow-experiment-method.Rd
man/numCodons.Rd
man/numExonsPerGroup.Rd
man/ofst_merge.Rd
man/optimizeReads.Rd
man/optimizedTranscriptLengths.Rd
man/optimized_txdb_path.Rd
man/orfFrameDistributions.Rd
man/orfID.Rd
man/orfScore.Rd
man/organism-experiment-method.Rd
man/outputLibs.Rd
man/pSitePlot.Rd
man/pasteDir.Rd
man/pcaExperiment.Rd
man/percentage_to_ratio.Rd
man/plotHelper.Rd
man/pmapFromTranscriptF.Rd
man/pmapToTranscriptF.Rd
man/prettyScoring.Rd
man/pseudo.transform.Rd
man/r-covRle-method.Rd
man/r.Rd
man/rankOrder.Rd
man/read.experiment.Rd
man/readBam.Rd
man/readBigWig.Rd
man/readLengthTable.Rd
man/readWidths.Rd
man/readWig.Rd
man/reassignTSSbyCage.Rd
man/reassignTxDbByCage.Rd
man/reduceKeepAttr.Rd
man/regionPerReadLength.Rd
man/remakeTxdbExonIds.Rd
man/remove.experiments.Rd
man/remove.file_ext.Rd
man/removeMetaCols.Rd
man/removeORFsWithSameStartAsCDS.Rd
man/removeORFsWithSameStopAsCDS.Rd
man/removeORFsWithStartInsideCDS.Rd
man/removeORFsWithinCDS.Rd
man/removeTxdbExons.Rd
man/removeTxdbTranscripts.Rd
man/rename.SRA.files.Rd
man/repNames.Rd
man/resFolder-experiment-method.Rd
man/resFolder.Rd
man/restrictTSSByUpstreamLeader.Rd
man/revElementsF.Rd
man/reverseMinusStrandPerGroup.Rd
man/riboORFs.Rd
man/riboORFsFolder.Rd
man/ribo_fft.Rd
man/ribo_fft_plot.Rd
man/ribosomeReleaseScore.Rd
man/ribosomeStallingScore.Rd
man/rnaNormalize.Rd
man/runIDs-experiment-method.Rd
man/runIDs.Rd
man/save.experiment.Rd
man/savePlot.Rd
man/scaledWindowPositions.Rd
man/scoreSummarizedExperiment.Rd
man/seqinfo-covRle-method.Rd
man/seqinfo-covRleList-method.Rd
man/seqinfo-experiment-method.Rd
man/seqlevels-covRle-method.Rd
man/seqlevels-covRleList-method.Rd
man/seqlevels-experiment-method.Rd
man/seqnamesPerGroup.Rd
man/shiftFootprints.Rd
man/shiftFootprintsByExperiment.Rd
man/shiftPlots.Rd
man/shifts.load.Rd
man/show-covRle-method.Rd
man/show-covRleList-method.Rd
man/show-experiment-method.Rd
man/simpleLibs.Rd
man/sortPerGroup.Rd
man/splitIn3Tx.Rd
man/stageNames.Rd
man/startCodons.Rd
man/startDefinition.Rd
man/startRegion.Rd
man/startRegionCoverage.Rd
man/startRegionString.Rd
man/startSites.Rd
man/stopCodons.Rd
man/stopDefinition.Rd
man/stopRegion.Rd
man/stopSites.Rd
man/strandBool.Rd
man/strandMode-covRle-method.Rd
man/strandMode-covRleList-method.Rd
man/strandPerGroup.Rd
man/subsetCoverage.Rd
man/subsetToFrame.Rd
man/symbols-experiment-method.Rd
man/symbols.Rd
man/te.plot.Rd
man/te.table.Rd
man/te_rna.plot.Rd
man/tile1.Rd
man/tissueNames.Rd
man/topMotif.Rd
man/transcriptWindow.Rd
man/transcriptWindow1.Rd
man/transcriptWindowPer.Rd
man/translationalEff.Rd
man/trim_detection.Rd
man/trimming.table.Rd
man/txNames.Rd
man/txNamesToGeneNames.Rd
man/txSeqsFromFa.Rd
man/uORFSearchSpace.Rd
man/uniqueGroups.Rd
man/uniqueOrder.Rd
man/unlistGrl.Rd
man/updateTxdbRanks.Rd
man/updateTxdbStartSites.Rd
man/upstreamFromPerGroup.Rd
man/upstreamOfPerGroup.Rd
man/validGRL.Rd
man/validSeqlevels.Rd
man/validateExperiments.Rd
man/widthPerGroup.Rd
man/windowCoveragePlot.Rd
man/windowPerGroup.Rd
man/windowPerReadLength.Rd
man/windowPerTranscript.Rd
man/xAxisScaler.Rd
man/yAxisScaler.Rd
src/.gitignore
src/RcppExports.cpp
src/findORFsHelpers.cpp
src/findORFsHelpers.h
src/findOrfs.cpp
src/findOrfsFasta.cpp
src/pmapFromTranscripts.cpp
src/pmapToTranscripts.cpp
tests/testthat.R
tests/testthat/test_DEG.R
tests/testthat/test_ORFs_helpers.R
tests/testthat/test_cage.R
tests/testthat/test_cds_helpers.R
tests/testthat/test_covRle.R
tests/testthat/test_coverage.R
tests/testthat/test_experiment.R
tests/testthat/test_features.R
tests/testthat/test_granges_helpers.R
tests/testthat/test_report.R
tests/testthat/test_shift_footprints.R
tests/testthat/test_utils.R
vignettes/Annotation_Alignment.Rmd
vignettes/Importing_Data.Rmd
vignettes/ORFikExperiment.Rmd
vignettes/ORFikOverview.Rmd
vignettes/Ribo-seq_pipeline.Rmd
vignettes/Working_with_transcripts.Rmd
