API for stianlagstad/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 Source code
import_function_non_ucsc	Man page Source code
import_fusioncatcher	Man page Source code
import_fusionmap	Man page Source code
import_infusion	Man page Source code
import_jaffa	Man page Source code
import_oncofuse	Man page Source code
import_prada	Man page Source code
import_soapfuse	Man page Source code
import_squid	Man page Source code
import_starfusion	Man page Source code
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