API for chimeraviz
Visualization tools for gene fusions

Global functions
.aeron_parse_data Source code
.check_that_breakpoints_are_within_transcripts Source code
.check_that_transcripts_have_breakpoint_exons Source code
.chimpipe_parse_junccoord Source code
.fusions_to_gene_label_data Man page Source code
.fusions_to_link_data Man page Source code
.get_transcripts_if_not_there Source code
.import_aeron_transcript_data Source code
.is_bamfile_bedgraphfile_valid Source code
.is_bamfile_valid Source code
.is_bamfile_valid_allow_null Source code
.is_bedfile_valid Source code
.is_bedgraphfile_valid Source code
.is_character_parameter_valid Source code
.is_edb_valid Source code
.is_fusion_valid Source code
.is_nucleotide_amount_valid Source code
.is_parameter_boolean Source code
.is_which_transcripts_valid Source code
.is_ylim_valid Source code
.scale_list_to_interval Man page Source code
.validate_plot_circle_params Source code
.validate_plot_fusion_params Source code
.validate_plot_fusion_reads_params Source code
.validate_plot_fusion_transcript_params Source code
.validate_plot_fusion_transcript_with_protein_domain_params Source code
.validate_plot_fusion_transcripts_graph_params Source code
.validate_plot_fusion_transcripts_params Source code
Fusion Man page
Fusion-class Man page
PartnerGene Man page
PartnerGene-class Man page
add_fusion_reads_alignment Man page Source code
chimeraviz Man page
chimeraviz-internals-fusions_to_gene_label_data Man page
chimeraviz-internals-fusions_to_link_data Man page
chimeraviz-internals-scaleListToInterval Man page
create_fusion_report Man page Source code
decide_transcript_category Man page Source code
down_shift Man page Source code
downstream_partner_gene Man page
downstream_partner_gene,Fusion-method Man page
downstream_partner_gene<- Man page
downstream_partner_gene<-,Fusion-method Man page
fetch_reads_from_fastq Man page Source code
fusion_spanning_reads_count Man page
fusion_spanning_reads_count,Fusion-method Man page
fusion_split_reads_count Man page
fusion_split_reads_count,Fusion-method Man page
fusion_to_data_frame Man page Source code
get_ensembl_ids Man page Source code
get_fusion_by_chromosome Man page Source code
get_fusion_by_gene_name Man page Source code
get_fusion_by_id Man page Source code
get_transcripts_ensembl_db Man page Source code
import_aeron Man page Source code
import_chimpipe Man page Source code
import_defuse Man page Source code
import_ericscript Man page
import_function_non_ucsc Man page
import_fusioncatcher Man page
import_fusionmap Man page
import_infusion Man page
import_jaffa Man page
import_oncofuse Man page
import_prada Man page
import_soapfuse Man page
import_squid Man page Source code
import_starfusion Man page
partner_gene_ensembl_id Man page
partner_gene_ensembl_id,PartnerGene-method Man page
partner_gene_ensembl_id<- Man page
partner_gene_ensembl_id<-,PartnerGene-method Man page
partner_gene_junction_sequence Man page
partner_gene_junction_sequence,PartnerGene-method Man page
plot_circle Man page Source code
plot_fusion Man page Source code
plot_fusion_reads Man page Source code
plot_fusion_separate Man page Source code
plot_fusion_together Man page Source code
plot_fusion_transcript Man page Source code
plot_fusion_transcript_with_protein_domain Man page Source code
plot_fusion_transcripts_graph Man page Source code
plot_transcripts Man page Source code
raw_Homo_sapiens.GRCh37.74 Man page
raw_chimpipe Man page
raw_cytobandhg19 Man page
raw_cytobandhg38 Man page
raw_defuse Man page
raw_ericscript Man page
raw_fusion5267proteindomains Man page
raw_fusion5267reads Man page
raw_fusion5267readsBedGraph Man page
raw_fusioncatcher Man page
raw_fusionmap Man page
raw_infusion Man page
raw_jaffa Man page
raw_oncofuse Man page
raw_prada Man page
raw_soapfuse Man page
raw_starfusion Man page
select_transcript Man page Source code
show,Fusion-method Man page
show,PartnerGene-method Man page
split_on_utr_and_add_feature Man page Source code
upstream_partner_gene Man page
upstream_partner_gene,Fusion-method Man page
upstream_partner_gene<- Man page
upstream_partner_gene<-,Fusion-method Man page
write_fusion_reference Man page Source code
chimeraviz documentation built on Nov. 8, 2020, 7:18 p.m.