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

Global functions
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
assignSubfeatureHits Source code
bubbles Man page
bubbles,ANY-method Man page
bubbles,IntegerList-method Man page
bubbles,SplicingGraphs-method Man page
bubbles-methods Man page
buildEdgeList2 Source code
build_sgedge2rsgedge_map Source code
build_sgedge2rsgedge_map_from_revfactor Source code
checkOrMakeUniqueGroupingNames Source code
check_all_edge_mcolnames Source code
check_assignSubfeatureHits_args Source code
check_exon_mcolnames Source code
check_reads_names 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
emptySplicingGraphs Source code
extract_bubbles_from_txpathmat Source code
extract_sgedges_exon_hits Source code
extract_sgedges_intron_hits Source code
fancy_punion Source code
find_old2new_mapping Source code
get_bubble_variants Source code
get_fq_uninfnodes Source code
get_index_of_group_of_mcols Source code
get_index_of_invariant_edge_mcols Source code
get_pEdge_fixed_attrs Source code
get_sgnodes_from_sgedges Source code
get_sgnodes_from_txpath Source code
get_sgnodetypes_from_txpathmat Source code
graph.to.graphNEL2 Source code
has_duplicates 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_edgeAttrs_from_graphNEL Source code
make_Ragraph_from_graphNEL Source code
make_Ragraph_from_igraph 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_global_sgedge_id 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_matrix_from_txpath Source code
make_revfactor_from_uninfnodes Source code
make_sgedges0_from_txpath Source code
make_sgedges_from_sgedges0 Source code
names,SplicingGraphs-method Man page
normargGrouping Source code
onLoad Source code
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
plotTranscripts.GRangesList Source code
precook_igraph_edges_from_sgedges Source code
reduce_edges Source code
removeReads Man page 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
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
s_bubble Source code
s_bubble2 Source code
safeTranslateAttrNames Source code
safeTranslateEdgeNames Source code
seqinfo,GeneModel-method Man page
seqinfo,SplicingGraphs-method Man page
seqnames,GeneModel-method Man page
seqnames,SplicingGraphs-method Man page
setSplicingGraphInfo Source code
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
singletons Source code
slideshow Man page Source code
strand,GeneModel-method Man page
strand,SplicingGraphs-method Man page
subsetByOverlapWithSingleRange Source code
test Source code
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.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
valid_exon_mcolnames Source code
Bioconductor/SplicingGraphs documentation built on Dec. 6, 2018, 1:09 p.m.