Man pages for ldg21/SGSeq
Splice event prediction and quantification from RNA-seq data
| analyzeFeatures | Analysis of splice graph features from BAM files |
| analyzeVariants | Analysis of splice variants |
| annotate | Annotation with respect to transcript features |
| annotateSGVariants | Annotate splice variants in terms of canonical events |
| assays | Accessing and replacing assay data |
| convertToSGFeatures | Convert transcript features to splice graph features |
| convertToTxFeatures | Convert to TxFeatures object |
| exonCompatible | Compatible fragment counts for exons |
| exportFeatures | Export to BED format |
| filterFeatures | Filter predicted features |
| findOverlapsRanges | Modified 'findOverlaps' function for 'IRanges', 'IRangesList'... |
| findSGVariants | Identify splice variants from splice graph |
| getBamInfo | Obtain library information from BAM files |
| getSGFeatureCounts | Compatible counts for splice graph features from BAM files |
| getSGFeatureCountsPerSample | Compatible fragment counts for splice graph features |
| getSGVariantCounts | Representative counts and frequency estimates for splice... |
| gr | Example genomic region of interest |
| importTranscripts | Import transcripts from GFF file |
| junctionCompatible | Compatible fragment counts for splice junctions |
| makeSGFeatureCounts | Create 'SGFeatureCounts' object |
| makeVariantNames | Create interpretable splice variant names |
| mergeTxFeatures | Merge redundant features |
| plotCoverage | Plot read coverage and splice junction read counts |
| plotFeatures | Plot splice graph and heatmap of expression values |
| plotSpliceGraph | Plot splice graph |
| plotVariants | Plot splice graph and heatmap of splice variant frequencies |
| predictCandidatesInternal | Identify candidate internal exons |
| predictCandidatesTerminal | Identify candidate terminal exons |
| predictExonsInternal | Identify internal exons |
| predictExonsTerminal | Identify terminal exons |
| predictJunctions | Identify splice junctions |
| predictSpliced | Ranges-based identification of splice junctions and exons |
| predictTxFeatures | Splice junction and exon prediction from BAM files |
| predictTxFeaturesPerSample | Identification of splice junctions and exons from BAM file |
| predictTxFeaturesPerStrand | Identification of splice junctions and exons for a given... |
| predictVariantEffects | Predict the effect of splice variants on protein-coding... |
| processTerminalExons | Process predicted terminal exons |
| removeExonsIsolated | Remove exons with no flanking splice junctions |
| sgf_ann | Example splice graph features (annotation-based) |
| sgfc_ann | Example splice graph feature counts (annotation-based) |
| sgfc_pred | Example splice graph feature counts (predicted) |
| SGFeatureCounts | Splice graph feature counts |
| SGFeatures | Splice graph features |
| sgf_pred | Example splice graph features (predicted) |
| SGSegments | Splice graph segments |
| sgv_ann | Example splice variants (annotation-based) |
| SGVariantCounts | Splice graph variant counts |
| SGVariants | Splice graph variants |
| sgvc_ann | Example splice variant counts (annotated) |
| sgvc_ann_from_bam | Example splice variant counts (annotated) from BAM files |
| sgvc_pred | Example splice variant counts (predicted) |
| sgvc_pred_from_bam | Example splice variant counts (predicted) from BAM files |
| sgv_pred | Example splice variants (predicted) |
| si | Example sample information |
| slots | Accessing and replacing metadata columns |
| splicesiteOverlap | Compatible fragment counts for splice sites |
| tx | Example transcripts |
| txf_ann | Example transcript features (annotation-based) |
| TxFeatures | Transcript features |
| txf_pred | Example transcript features (predicted) |
| updateObject | Update object |
