SplicingGraphs
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Package index
Search the SplicingGraphs package
Vignettes
Functions
179
Source code
20
Man pages
13
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SplicingGraphs: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
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API

API for SplicingGraphs
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Global functions
.assignSubfeatureHits Source code
.buildEdgeList2 Source code
.build_sgedge2rsgedge_map Source code
.build_sgedge2rsgedge_map_from_revfactor Source code
.checkOrMakeUniqueGroupingNames Source code
.check_assignSubfeatureHits_args Source code
.check_reads_names Source code
.extract_bubbles_from_txpathmat Source code
.extract_sgedges_exon_hits Source code
.extract_sgedges_intron_hits Source code
.find_old2new_mapping Source code
.get_bubble_variants Source code
.get_fq_uninfnodes Source code
.get_pEdge_fixed_attrs Source code
.get_sgnodes_from_sgedges Source code
.get_sgnodetypes_from_txpathmat Source code
.has_duplicates Source code
.igraph.to.graphNEL2 Source code
.is_bubble Source code
.is_bubble2 Source code
.make_Ragraph_edgeAttrs_from_graphNEL Source code
.make_Ragraph_from_graphNEL Source code
.make_Ragraph_nodeAttrs_from_graphNEL Source code
.make_SSids Source code
.make_bit_strings_from_logical_matrix Source code
.make_ex_by_tx_from_GRangesList Source code
.make_factor_from_revfactor Source code
.make_igraph Source code
.make_igraph_from_sgedges Source code
.make_igraph_from_sgedges0 Source code
.make_logical_matrix_from_bit_strings Source code
.make_revfactor_from_uninfnodes Source code
.make_sgedges0_from_txpath Source code
.make_sgedges_from_sgedges0 Source code
.normarg_grouping Source code
.onLoad Source code
.plotTranscripts.GRangesList Source code
.precook_igraph_edges_from_sgedges Source code
.reduce_edges Source code
.remove_uninformative_SSids Source code
.repair_edge_data Source code
.reportReads_by_gene Source code
.reportReads_by_rsgedge Source code
.reportReads_by_sgedge Source code
.reportReads_by_tx Source code
.safeTranslateAttrNames Source code
.safeTranslateEdgeNames Source code
.set_splicing_graph_info Source code
.singletons Source code
.subsetByOverlapWithSingleRange Source code
.test Source code
.valid.GeneModel Source code
.valid.GeneModel.ex_by_tx Source code
.valid.GeneModel.names Source code
.valid.SplicingGraphs Source code
.valid.SplicingGraphs.in_by_tx Source code
ASCODE2DESC Man page
GeneModel Source code
GeneModel-class Man page
SplicingGraphs Man page
SplicingGraphs,GRangesList-method Man page
SplicingGraphs,TxDb-method Man page
SplicingGraphs-class Man page
SplicingGraphs-package Man page
TSPC Man page
TSPCsg Man page
[,SplicingGraphs,ANY,ANY-method Man page
[[,SplicingGraphs,ANY,ANY-method Man page
assignReads Man page Source code
bubbles Man page
bubbles,ANY-method Man page
bubbles,IntegerList-method Man page
bubbles,SplicingGraphs-method Man page
bubbles-methods Man page
check_all_edge_mcolnames Source code
check_exon_mcolnames Source code
class:GeneModel Man page
class:SplicingGraphs Man page
commonSeqnames.GRangesList Source code
commonSeqnames.RleList Source code
commonStrand.GRanges Source code
commonStrand.GRangesList Source code
commonStrand.RleList Source code
countReads Man page
countReads,SplicingGraphs-method Man page
countReads-methods Man page
elementNROWS,SplicingGraphs-method Man page
fancy_punion Source code
get_index_of_group_of_mcols Source code
get_index_of_invariant_edge_mcols Source code
get_sgnodes_from_txpath Source code
indeg Man page
indeg,ANY-method Man page
indeg,DataFrame-method Man page
intronsByTranscript,SplicingGraphs-method Man page
isCircular<-,GeneModel-method Man page
isCircular<-,SplicingGraphs-method Man page
layout.sgraph Source code
length,SplicingGraphs-method Man page
make_Ragraph_from_igraph Source code
make_empty_SplicingGraphs Source code
make_global_sgedge_id Source code
make_matrix_from_txpath Source code
names,SplicingGraphs-method Man page
outdeg Man page
outdeg,ANY-method Man page
outdeg,DataFrame-method Man page
plot,SplicingGraphs,missing-method Man page
plotTranscripts Man page
plotTranscripts,GRangesList-method Man page
plotTranscripts,SplicingGraphs-method Man page
plotTranscripts,TxDb-method Man page
plotTranscripts-methods Man page
removeReads Man page Source code
rsgedges Man page Source code
rsgedgesByGene Man page
rsgedgesByGene,SplicingGraphs-method Man page
rsgedgesByGene-methods Man page
rsgedgesByTranscript Man page
rsgedgesByTranscript,SplicingGraphs-method Man page
rsgraph Man page Source code
seqinfo,GeneModel-method Man page
seqinfo,SplicingGraphs-method Man page
seqnames,GeneModel-method Man page
seqnames,SplicingGraphs-method Man page
sgedges Man page
sgedges,SplicingGraphs-method Man page
sgedges-methods Man page
sgedges2 Man page
sgedgesByGene Man page
sgedgesByGene,SplicingGraphs-method Man page
sgedgesByGene-methods Man page
sgedgesByTranscript Man page
sgedgesByTranscript,SplicingGraphs-method Man page
sgnodes Man page
sgnodes,DataFrame-method Man page
sgnodes,IntegerList-method Man page
sgnodes,SplicingGraphs-method Man page
sgnodes,data.frame-method Man page
sgraph Man page
sgraph,ANY-method Man page
sgraph,DataFrame-method Man page
sgraph,data.frame-method Man page
sgraph,igraph-method Man page
sgraph-methods Man page
sgraph2 Man page
show,SplicingGraphs-method Man page
slideshow Man page Source code
strand,GeneModel-method Man page
strand,SplicingGraphs-method Man page
toy_data Man page
toy_genes_gff Man page Source code
toy_overlaps Man page Source code
toy_reads_bam Man page Source code
toy_reads_sam Man page Source code
txpath Man page
txpath,GRangesList-method Man page
txpath,SplicingGraphs-method Man page
txpath-methods Man page
txweight Man page
txweight,SplicingGraphs-method Man page
txweight<- Man page
txweight<-,SplicingGraphs-method Man page
uninformativeSSids Man page
uninformativeSSids,ANY-method Man page
uninformativeSSids,DataFrame-method Man page
uninformative_sgnodes Source code
unlist,SplicingGraphs-method Man page
unlistAndSplit Source code
valid_exon_mcolnames Source code
SplicingGraphs documentation built on Nov. 8, 2020, 5:58 p.m.

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