SplicingGraphs: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Version 1.16.0

This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.

Browse man pages Browse package API and functions Browse package files

AuthorD. Bindreither, M. Carlson, M. Morgan, H. Pagès
Bioconductor views AlternativeSplicing Annotation DataRepresentation GeneExpression Genetics RNASeq Sequencing Transcription Visualization
Date of publicationNone
MaintainerH. Pagès <hpages@fredhutch.org>
LicenseArtistic-2.0
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SplicingGraphs")

Man pages

assignReads: Assign reads to the edges of a SplicingGraphs object
bubbles-methods: Compute the bubbles of a splicing graph
countReads-methods: Summarize the reads assigned to a SplicingGraphs object
plotTranscripts-methods: Plot a set of transcripts along genomic coordinates.
rsgedgesByGene-methods: Extract the reduced edges and their ranges from a...
sgedgesByGene-methods: Extract the edges and their ranges from a SplicingGraphs...
sgedges-methods: Extract the edges (and nodes) of a splicing graph
sgraph-methods: Extract a splicing graph as a plottable graph-like object
SplicingGraphs-class: SplicingGraphs objects
SplicingGraphs-package: Create, manipulate, visualize splicing graphs, and assign...
toy_data: Little helpers for quick access to the toy data included in...
TSPCsg: TSPC splicing graphs
txpath-methods: Extract the transcript paths of a splicing graph

Functions

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
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

Files

.Rinstignore
DESCRIPTION
NAMESPACE
R
R/SplicingGraphs-class.R
R/assignReads.R
R/bubbles-methods.R
R/countReads-methods.R
R/igraph-utils.R
R/plotTranscripts-methods.R
R/rsgedgesByGene-methods.R
R/sgedges-methods.R
R/sgedgesByGene-methods.R
R/sgraph-methods.R
R/toy_data.R
R/txpath-methods.R
R/utils.R
R/zzz.R
TODO
build
build/vignette.rds
inst
inst/doc
inst/doc/SplicingGraphs.R
inst/doc/SplicingGraphs.Rnw
inst/doc/SplicingGraphs.pdf
inst/extdata
inst/extdata/ASpatterns.txt
inst/extdata/TSPCsg.rda
inst/extdata/toy_genes.gff3
inst/extdata/toy_overlaps.txt
inst/extdata/toy_reads.sam
inst/scripts
inst/scripts/TSPC-utils.R
inst/scripts/create-vignette-plots.R
inst/scripts/makeTSPCsg.R
inst/unitTests
inst/unitTests/test_countReads-methods.R
man
man/SplicingGraphs-class.Rd
man/SplicingGraphs-package.Rd
man/TSPCsg.Rd
man/assignReads.Rd
man/bubbles-methods.Rd
man/countReads-methods.Rd
man/plotTranscripts-methods.Rd
man/rsgedgesByGene-methods.Rd
man/sgedges-methods.Rd
man/sgedgesByGene-methods.Rd
man/sgraph-methods.Rd
man/toy_data.Rd
man/txpath-methods.Rd
tests
tests/run_unitTests.R
vignettes
vignettes/SplicingGraphs.Rnw
vignettes/images
vignettes/images/CIB3-sg.pdf
vignettes/images/CIB3-sg2.pdf
vignettes/images/CIB3-transcripts.pdf
vignettes/images/ZNF813-sg.pdf
vignettes/images/ZNF813-sg2.pdf
vignettes/images/ZNF813-transcripts.pdf
vignettes/precomputed_results
vignettes/precomputed_results/sg_with_bubbles.rda
vignettes/precomputed_results/sg_with_reads.rda
SplicingGraphs documentation built on May 20, 2017, 9:59 p.m.