Package: chimeraviz 1.31.0

Stian Lågstad

chimeraviz: Visualization tools for gene fusions

chimeraviz manages data from fusion gene finders and provides useful visualization tools.

Authors:Stian Lågstad [aut, cre], Sen Zhao [ctb], Andreas M. Hoff [ctb], Bjarne Johannessen [ctb], Ole Christian Lingjærde [ctb], Rolf Skotheim [ctb]

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NEWS

# Install 'chimeraviz' in R:
install.packages('chimeraviz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/stianlagstad/chimeraviz/issues

On BioConductor:chimeraviz-1.31.0(bioc 3.20)chimeraviz-1.30.0(bioc 3.19)

bioconductor-package

45 exports 1.00 score 163 dependencies 2 mentions

Last updated 2 months agofrom:e57f666d98

Exports:add_fusion_reads_alignmentcreate_fusion_reportdecide_transcript_categorydown_shiftdownstream_partner_genedownstream_partner_gene<-fetch_reads_from_fastqfusion_spanning_reads_countfusion_split_reads_countfusion_to_data_frameget_ensembl_idsget_fusion_by_chromosomeget_fusion_by_gene_nameget_fusion_by_idget_transcripts_ensembl_dbimport_aeronimport_chimpipeimport_defuseimport_ericscriptimport_fusioncatcherimport_fusionmapimport_infusionimport_jaffaimport_oncofuseimport_pradaimport_soapfuseimport_squidimport_starfusionpartner_gene_ensembl_idpartner_gene_ensembl_id<-partner_gene_junction_sequenceplot_circleplot_fusionplot_fusion_readsplot_fusion_separateplot_fusion_togetherplot_fusion_transcriptplot_fusion_transcript_with_protein_domainplot_fusion_transcripts_graphplot_transcriptsselect_transcriptsplit_on_utr_and_add_featureupstream_partner_geneupstream_partner_gene<-write_fusion_reference

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocStylebiomaRtBiostringsbiovizBasebitbit64bitopsblobbookdownBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrDTensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegraphgridExtragtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslorg.Hs.eg.dborg.Mm.eg.dbpillarpkgconfigplogrplyrpngprettyunitsprogresspromisesProtGenericspurrrR6rappdirsRCircosRColorBrewerRcppRcppEigenRCurlrestfulrRgraphvizRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

chimeraviz

Stian Lågstad

Rendered fromchimeraviz-vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2019-03-17
Started: 2016-12-12

Readme and manuals

Help Manual

Help pageTopics
Add fusion reads alignment to fusion objectadd_fusion_reads_alignment
chimeraviz: A package for working with and visualizing fusion genes.chimeraviz
Create gene label data for RCircos from the given fusions..fusions_to_gene_label_data chimeraviz-internals-fusions_to_gene_label_data
Create link data for RCircos from the given fusions..fusions_to_link_data chimeraviz-internals-fusions_to_link_data
Scale a vector of numeric values to an interval..scale_list_to_interval chimeraviz-internals-scaleListToInterval
Create a Fusion Reportcreate_fusion_report
Retrieves transcripts for partner genes in a Fusion object using Ensembldbdecide_transcript_category
Remove introns and shift exons leftwarddown_shift
Get the downstream fusion partner genedownstream_partner_gene downstream_partner_gene,Fusion-method downstream_partner_gene<- downstream_partner_gene<-,Fusion-method
Fetch reads from fastq filesfetch_reads_from_fastq
Get the spanning reads count from a Fusion objectfusion_spanning_reads_count fusion_spanning_reads_count,Fusion-method
Get the split reads count from a Fusion objectfusion_split_reads_count fusion_split_reads_count,Fusion-method
Coerce Fusion object to data.framefusion_to_data_frame
An S4 class to represent a fusion event.Fusion Fusion-class
Get ensembl ids for a fusion objectget_ensembl_ids
Find fusions that involves genes in the given chromosome.get_fusion_by_chromosome
Find fusions that includes the given gene.get_fusion_by_gene_name
Find a specific fusion object in a list by idget_fusion_by_id
Retrieves transcripts for partner genes in a Fusion object using Ensembldbget_transcripts_ensembl_db
Import results from an Aeron run into a list of Fusion objects.import_aeron
Import results from a ChimPipe run into a list of Fusion objects.import_chimpipe
Import results from a deFuse run into a list of Fusion objects.import_defuse
Import results from a EricScript run into a list of Fusion objects.import_ericscript
Alternative import function for Gviz::AlignmentsTrackimport_function_non_ucsc
Import results from a Fusioncatcher run into a list of Fusion objects.import_fusioncatcher
Import results from a FusionMap run into a list of Fusion objects.import_fusionmap
Import results from an InFusion run into a list of Fusion objects.import_infusion
Import results from a JAFFA run into a list of Fusion objects.import_jaffa
Import results from a oncofuse run into a list of Fusion objects.import_oncofuse
Import results from a PRADA run into a list of Fusion objects.import_prada
Import results from a SOAPfuse run into a list of Fusion objects.import_soapfuse
Import results from a SQUID run into a list of Fusion objects.import_squid
Import results from a STAR-Fusion run into a list of Fusion objects.import_starfusion
Get the Ensembl ID from a PartnerGene objectpartner_gene_ensembl_id partner_gene_ensembl_id,PartnerGene-method partner_gene_ensembl_id<- partner_gene_ensembl_id<-,PartnerGene-method
Get the junction sequence from a PartnerGene objectpartner_gene_junction_sequence partner_gene_junction_sequence,PartnerGene-method
An S4 class to represent a gene partner in a fusionPartnerGene PartnerGene-class
Create a circle plot of the given fusions.plot_circle
Plot a fusion event with transcripts, coverage and ideograms.plot_fusion plot_fusion_separate plot_fusion_together
Create a plot of the reads supporting the given fusion.plot_fusion_reads
Plot possible fusion transcripts based on annotation.plot_fusion_transcript
Plot a specific fusion transcript with protein domain annotationsplot_fusion_transcript_with_protein_domain
Graph plot of possible fusion transcripts.plot_fusion_transcripts_graph
Plot transcripts for each partner gene in a fusion event.plot_transcripts
ChimPipe dataraw_chimpipe
Cytoband information HG19raw_cytobandhg19
Cytoband information HG138raw_cytobandhg38
deFuse dataraw_defuse
EricScript dataraw_ericscript
protein_domains_5267 bed fileraw_fusion5267proteindomains
Fusion5267and11759 bamfileraw_fusion5267reads
Fusion5267and11759 bedGraph fileraw_fusion5267readsBedGraph
Fusioncatcher dataraw_fusioncatcher
FusionMap dataraw_fusionmap
Homo_sapiens.GRCh37.74_subset.gtfraw_Homo_sapiens.GRCh37.74
InFusion dataraw_infusion
JAFFA dataraw_jaffa
oncofuse dataraw_oncofuse
PRADA dataraw_prada
SOAPfuse dataraw_soapfuse
STAR-Fusion dataraw_starfusion
Select which transcript to use (for plotting) for a GenePartner objectselect_transcript
Show method for the Fusion class.show,Fusion-method
Show method for the PartnerGene class.show,PartnerGene-method
Split GRanges object based on cdssplit_on_utr_and_add_feature
Get the upstream fusion partner geneupstream_partner_gene upstream_partner_gene,Fusion-method upstream_partner_gene<- upstream_partner_gene<-,Fusion-method
Write fusion junction sequence to a fasta filewrite_fusion_reference