Man pages for jmw86069/splicejam
Analysis and Visualization of Gene Splice Variants and Transcriptome Data

addGRgapsAdd gaps between GRanges regions
addGRLgapsAdd gaps between GRangesList regions
ale2violinPrepare ALE data for violin plots
annotateGRfromGRAnnotate GRanges using another GRanges object
annotateGRLfromGRLAnnotate GRangesList from GRangesList objects
assignGRLexonNamesAssign exon names to GRangesList
bgaPlotly3dCreate an interactive 3-D BGA plotly visualization
closestExonToJunctionsFind closest exon to splice junction ends
codonUsage2dfMake codon usage data.frame
combineGRcoverageCombine GRanges coverage replicates
compressPolygonMCompress genome coordinates of a matrix of polygons
curateDFtoDFCurate data.frame into a data.frame
curateVtoDFCurate vector into a data.frame
defineDetectedTxDefine detected transcripts
detectedTxInfoSummarize detected transcript results
df2colorSubConvert data.frame to categorical colors
dfWide2segmentsConvert data.frame to plotly line segment format
dna2codonConvert DNA to 3-base codons
escapeWhitespaceRegexpEscape whitespace in regular expression patterns
exoncov2polygonConvert exon coverage to polygons
factor2labelConvert factor to a factor label
findOverlapsGRLFind overlaps between two GRangesList objects
flattenExonsByFlatten exons by gene or transcript
gene2ggGene GRangesList to ggplot2 grob
geom_diagonal_wide_arcDraw an area defined by an upper and lower diagonal into an...
geomeanClassical geometric mean
getFirstStrandedFromGRLGet first stranded GRanges feature per GRangesList
get_fn_envirGet value from function call or specific environment
getGRcoverageFromBwGet coverage for GRanges from bigWig files
getGRgapsGet gaps in GRanges
getGRLgapsGet gaps in GRangesList objects
grl2dfGRangesList to data.frame for ggplot2
groups2contrastsDefine experimental contrasts from sample groups
import_juncs_from_bedImport splice junction data from BED or file
intercalateIntercalate list values into a vector
internal_junc_scoremaximum overlapping internal junction score
jamCaiCalculate Codon Adaptation Index
jamGeomeanModified geometric mean for positive and negative values
jam_isDisjointTest whether GRanges are disjoint (non-overlapping)
jitter_normApply jitter using normal distribution
launchSashimiAppLaunch Sashimi R-shiny application
list2imConvert list to incidence matrix
make_ref2compressedCreate a ref2compressed function to compress GR gaps
makeTx2geneFromGtfMake tx2gene data.frame from a GTF file
plotSashimiJam Sashimi plot
prepareSashimiPrepare Sashimi plot data
psl2dfConvert PSL alignment to data.frame
runDiffSplicePerform differential isoform analysis using diffSplice
sashimiAppConstantsSashimi Shiny app constants
sashimiAppServerSashimi Shiny app server
sashimiAppUISashimi Shiny app UI
sashimiDataConstantsPrepare sashimi plot required data
shrinkMatrixShrink numeric matrix by groups of rows
simplifyXYSimplify XY coordinates to minimal line segments
sortGRLSort GRangesList elements by chromosome and position
sortSamplesSort biological sample labels for experimental design
spliceGR2junctionDFSplice junction data.frame summary
splicejam-extensionssplicejam extensions to ggforce
spline3dCalculate a spline curve fit in 3-D
stackJunctionsStack the y-axis position of junctions
strsplitOrderedSplit the elements of an ordered factor vector
test_cov_grSample exon coverage data GRanges
test_cov_wide_grSample exon coverage data GRanges with wide introns
test_exon_grSample exon data GRanges
test_exon_wide_grSample exon data GRanges with wide introns
test_junc_grSample junction data GRangesList
test_junc_wide_grSample junction data GRangesList with wide introns
to_basic.GeomShapeSupport plotly for GeomShape
tx2aletx2ale: detect alternative last exons (ALE) from transcript...
jmw86069/splicejam documentation built on Aug. 10, 2021, 6:27 p.m.