Convert to TxFeatures object
Accessing and replacing assay data
Annotate splice variants in terms of canonical events
Filter predicted features
Convert transcript features to splice graph features
Annotation with respect to transcript features
Export to BED format
Analysis of splice graph features from BAM files
Analysis of splice variants
Compatible fragment counts for exons
getSGFeatureCountsPerSample
Compatible fragment counts for splice graph features
Representative counts and frequency estimates for
splice variants
Modified findOverlaps
function for IRanges
,
IRangesList
objects
Identify splice variants from splice graph
Compatible counts for splice graph features from BAM files
Obtain library information from BAM files
Import transcripts from GFF file
Example genomic region of interest
Compatible fragment counts for splice junctions
Create SGFeatureCounts
object
Plot read coverage and splice junction read counts
Plot splice graph and heatmap of expression values
predictTxFeaturesPerStrand
Identification of splice junctions and exons for a given
chromosome and strand
Example splice graph feature counts (annotation-based)
Predict the effect of splice variants on protein-coding transcripts
Example splice graph feature counts (predicted)
Identify splice junctions
Ranges-based identification of splice junctions and exons
Splice graph segments
Example splice variants (annotation-based)
Example transcripts
Example transcript features (annotation-based)
Plot splice graph
Plot splice graph and heatmap of splice variant frequencies
Example sample information
Example splice variant counts (predicted)
Example splice graph features (annotation-based)
Example splice graph features (predicted)
Splice graph feature counts
Splice graph features
Identify internal exons
Splice graph variants
Accessing and replacing metadata columns
Compatible fragment counts for splice sites
Example splice variant counts (annotated) from BAM files
Identify terminal exons
Splice junction and exon prediction from BAM files
Create interpretable splice variant names
Merge redundant features
predictTxFeaturesPerSample
Identification of splice junctions and exons from BAM file
Splice graph variant counts
Example splice variant counts (annotated)
Example splice variants (predicted)
Example splice variant counts (predicted) from BAM files
predictCandidatesInternal
Identify candidate internal exons
predictCandidatesTerminal
Identify candidate terminal exons
Process predicted terminal exons
Remove exons with no flanking splice junctions
Example transcript features (predicted)
Transcript features
Update object