Man pages for chimeraviz
Visualization tools for gene fusions
| add_fusion_reads_alignment | Add fusion reads alignment to fusion object |
| chimeraviz | chimeraviz: A package for working with and visualizing fusion... |
| chimeraviz-internals-fusions_to_gene_label_data | Create gene label data for RCircos from the given fusions. |
| chimeraviz-internals-fusions_to_link_data | Create link data for RCircos from the given fusions. |
| chimeraviz-internals-scaleListToInterval | Scale a vector of numeric values to an interval. |
| create_fusion_report | Create a Fusion Report |
| decide_transcript_category | Retrieves transcripts for partner genes in a Fusion object... |
| down_shift | Remove introns and shift exons leftward |
| downstream_partner_gene | Get the downstream fusion partner gene |
| fetch_reads_from_fastq | Fetch reads from fastq files |
| Fusion-class | An S4 class to represent a fusion event. |
| fusion_spanning_reads_count | Get the spanning reads count from a Fusion object |
| fusion_split_reads_count | Get the split reads count from a Fusion object |
| fusion_to_data_frame | Coerce Fusion object to data.frame |
| get_ensembl_ids | Get ensembl ids for a fusion object |
| get_fusion_by_chromosome | Find fusions that involves genes in the given chromosome. |
| get_fusion_by_gene_name | Find fusions that includes the given gene. |
| get_fusion_by_id | Find a specific fusion object in a list by id |
| get_transcripts_ensembl_db | Retrieves transcripts for partner genes in a Fusion object... |
| import_aeron | Import results from an Aeron run into a list of Fusion... |
| import_chimpipe | Import results from a ChimPipe run into a list of Fusion... |
| import_defuse | Import results from a deFuse run into a list of Fusion... |
| import_ericscript | Import results from a EricScript run into a list of Fusion... |
| import_function_non_ucsc | Alternative import function for Gviz::AlignmentsTrack |
| import_fusioncatcher | Import results from a Fusioncatcher run into a list of Fusion... |
| import_fusionmap | Import results from a FusionMap run into a list of Fusion... |
| import_infusion | Import results from an InFusion run into a list of Fusion... |
| import_jaffa | Import results from a JAFFA run into a list of Fusion... |
| import_oncofuse | Import results from a oncofuse run into a list of Fusion... |
| import_prada | Import results from a PRADA run into a list of Fusion... |
| import_soapfuse | Import results from a SOAPfuse run into a list of Fusion... |
| import_squid | Import results from a SQUID run into a list of Fusion... |
| import_starfusion | Import results from a STAR-Fusion run into a list of Fusion... |
| PartnerGene-class | An S4 class to represent a gene partner in a fusion |
| partner_gene_ensembl_id | Get the Ensembl ID from a PartnerGene object |
| partner_gene_junction_sequence | Get the junction sequence from a PartnerGene object |
| plot_circle | Create a circle plot of the given fusions. |
| plot_fusion | Plot a fusion event with transcripts, coverage and ideograms. |
| plot_fusion_reads | Create a plot of the reads supporting the given fusion. |
| plot_fusion_transcript | Plot possible fusion transcripts based on annotation. |
| plot_fusion_transcripts_graph | Graph plot of possible fusion transcripts. |
| plot_fusion_transcript_with_protein_domain | Plot a specific fusion transcript with protein domain... |
| plot_transcripts | Plot transcripts for each partner gene in a fusion event. |
| raw_chimpipe | ChimPipe data |
| raw_cytobandhg19 | Cytoband information HG19 |
| raw_cytobandhg38 | Cytoband information HG138 |
| raw_defuse | deFuse data |
| raw_ericscript | EricScript data |
| raw_fusion5267proteindomains | protein_domains_5267 bed file |
| raw_fusion5267reads | Fusion5267and11759 bamfile |
| raw_fusion5267readsBedGraph | Fusion5267and11759 bedGraph file |
| raw_fusioncatcher | Fusioncatcher data |
| raw_fusionmap | FusionMap data |
| raw_Homo_sapiens.GRCh37.74 | Homo_sapiens.GRCh37.74_subset.gtf |
| raw_infusion | InFusion data |
| raw_jaffa | JAFFA data |
| raw_oncofuse | oncofuse data |
| raw_prada | PRADA data |
| raw_soapfuse | SOAPfuse data |
| raw_starfusion | STAR-Fusion data |
| select_transcript | Select which transcript to use (for plotting) for a... |
| show-Fusion-method | Show method for the Fusion class. |
| show-PartnerGene-method | Show method for the PartnerGene class. |
| split_on_utr_and_add_feature | Split GRanges object based on cds |
| upstream_partner_gene | Get the upstream fusion partner gene |
| write_fusion_reference | Write fusion junction sequence to a fasta file |
