FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data


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Documentation for package ‘FLAMES’ version 1.0.2

Help Pages

bulk_long_pipeline Pipeline for Bulk Data
bulk_windows_pipeline_setup FLAMES Windows Bulk Pipeline
callBasilisk Internal utility function for simplifying calls to basiliskRun using a given basilisk environment
create_config Create Configuration File From Arguments
generate_umap Generate UMAP plot
generic_long_pipeline Generic FLAMES pipeline
get_default_config_file Default Configuration File
gff3_to_bed12 GFF3 to BED12
match_cell_barcode Match Cell Barcodes
merge_bulk_fastq Merge FASTQ
merge_bulk_fastq_cpp Merge Bulk Fastq Files
merge_bulk_fastq_python Merge FASTQ using python. Depreciated
minimap2_align Minimap2 Align to Genome
minimap2_check_callable Check if minimap2 is available
parse_gff_tree Parse Gff3 file
parse_json_config Parse Json Configuration File
print_config Print Configuration File
samtools_as_bam Samtools as BAM
samtools_sort_index Samtools Sort and Index
sc_DTU_analysis FLAMES Differential Transcript Usage Analysis
sc_long_pipeline Pipeline for Single Cell Data
sc_mutations FLAMES variant calling
sc_windows_pipeline_setup Windows Single Cell FLAMES Pipeline
windows_pipeline_isoforms Windows Pipeline - Find Isoforms
windows_pipeline_quantification Windows Pipeline - Quantification
write_config Write Configuration Dictionary to File