Man pages for jennylsmith/fusBreakpoint
Find fusion exon junction sequence reads from RNAseq BAM files
| calc_KMcurve_pvalues | Calculate the p-value for differnces in KM curves from... |
| coxSummaryTable | Create a dataframe output to summarize the results of Cox... |
| create_custom_pdict | Create Biostrings pdict (pattern dictionary) from a dataframe... |
| define_exon_junctions | Provides Exon Number from Genomic Coordinates. |
| examine_breakpoint_evidence | Workflow wrapper to extract RNAseq reads and search for... |
| fusion_category | Define Fusion Category for Harmonization Steps |
| genome_paint_format | Create JSON file for input into St. Jude Genome Paint |
| match_reads_contigs | Sequence pattern matching of RNAseq reads and counts the... |
| mcol_intron_rank | Add Intron Rank Column to GRanges containing gene introns |
| order_breakpoints | Order breakpoints Numerically for harmonization steps |
| outcome_table | Create a table with OS/EFS percent at specified time point |
| pipe | Pipe operator |
| risk.table | Title |
| subset_bam | Subset a bam for specific chromome(s) or ranges based on... |
| SurvivalPlot | Create Kaplan-Meier plots |
