Man pages for jmw86069/splicejam
Analysis and Visualization of Gene Splice Variants and Transcriptome Data
| addGRgaps | Add gaps between GRanges regions |
| addGRLgaps | Add gaps between GRangesList regions |
| ale2violin | Prepare ALE data for violin plots |
| annotateGRfromGR | Annotate GRanges using another GRanges object |
| annotateGRLfromGRL | Annotate GRangesList from GRangesList objects |
| assignGRLexonNames | Assign exon names to GRangesList |
| bgaPlotly3d | Create an interactive 3-D BGA plotly visualization |
| closestExonToJunctions | Find closest exon to splice junction ends |
| codonUsage2df | Make codon usage data.frame |
| combineGRcoverage | Combine GRanges coverage replicates |
| compressPolygonM | Compress genome coordinates of a matrix of polygons |
| curateDFtoDF | Curate data.frame into a data.frame |
| curateVtoDF | Curate vector into a data.frame |
| defineDetectedTx | Define detected transcripts |
| describeGtfAttrNames | describe gtf/gff3 attribute names |
| detectedTxInfo | Summarize detected transcript results |
| df2colorSub | Convert data.frame to categorical colors |
| dfWide2segments | Convert data.frame to plotly line segment format |
| dna2codon | Convert DNA to 3-base codons |
| escapeWhitespaceRegexp | Escape whitespace in regular expression patterns |
| exoncov2polygon | Convert exon coverage to polygons |
| factor2label | Convert factor to a factor label |
| findOverlapsGRL | Find overlaps between two GRangesList objects |
| flattenExonsBy | Flatten exons by gene or transcript |
| gene2gg | Gene GRangesList to ggplot2 grob |
| geom_diagonal_wide_arc | Draw an area defined by an upper and lower diagonal into an... |
| geomean | Classical geometric mean |
| getFirstStrandedFromGRL | Get first stranded GRanges feature per GRangesList |
| get_fn_envir | Get value from function call or specific environment |
| getGRcoverageFromBw | Get coverage for GRanges from bigWig files |
| getGRgaps | Get gaps in GRanges |
| getGRLgaps | Get gaps in GRangesList objects |
| grl2df | GRangesList to data.frame for ggplot2 |
| groups2contrasts | Define experimental contrasts from sample groups |
| import_juncs_from_bed | Import splice junction data from BED or SJ.out.tab file |
| intercalate | Intercalate list values into a vector |
| internal_junc_score | maximum overlapping internal junction score |
| jamCai | Calculate Codon Adaptation Index |
| jamGeomean | Modified geometric mean for positive and negative values |
| jam_isDisjoint | Test whether GRanges are disjoint (non-overlapping) |
| jitter_norm | Apply jitter using normal distribution |
| launchSashimiApp | Launch Sashimi R-shiny application |
| list2im | Convert list to incidence matrix |
| make_ref2compressed | Create a ref2compressed function to compress GR gaps |
| makeTx2geneFromGtf | Make tx2gene data.frame from a GTF file |
| plotSashimi | Jam Sashimi plot |
| prepareSashimi | Prepare Sashimi plot data |
| psl2df | Convert PSL alignment to data.frame |
| readGtf | read gtf/gff3 file |
| runDiffSplice | Perform differential isoform analysis using diffSplice |
| sashimiAppConstants | Sashimi Shiny app constants |
| sashimiAppServer | Sashimi Shiny app server |
| sashimiAppUI | Sashimi Shiny app UI |
| sashimiDataConstants | Prepare sashimi plot required data |
| shrinkMatrix | Shrink numeric matrix by groups of rows |
| simplifyXY | Simplify XY coordinates to minimal line segments |
| sortGRL | Sort GRangesList elements by chromosome and position |
| sortSamples | Sort biological sample labels for experimental design |
| spliceGR2junctionDF | Splice junction data.frame summary |
| splicejam-extensions | splicejam extensions to ggforce |
| spline3d | Calculate a spline curve fit in 3-D |
| stackJunctions | Stack the y-axis position of junctions |
| strsplitOrdered | Split the elements of an ordered factor vector |
| test_cov_gr | Sample exon coverage data GRanges |
| test_cov_wide_gr | Sample exon coverage data GRanges with wide introns |
| test_exon_gr | Sample exon data GRanges |
| test_exon_wide_gr | Sample exon data GRanges with wide introns |
| test_junc_gr | Sample junction data GRangesList |
| test_junc_wide_gr | Sample junction data GRangesList with wide introns |
| to_basic.GeomShape | Support plotly for GeomShape |
| tx2ale | tx2ale: detect alternative last exons (ALE) from transcript... |
