Man pages for McGranahanLab/TcellExTRECT
T cell Exome TREC Tool
| adjustTcellExTRECT | Adjust TCRA T cell fraction based on tumour purity and copy... |
| baselineAdj | Calculate median values of coverage within exons in rolling... |
| calcQCvalue | Method for calculating QC values to judge GAM fit |
| cov_example | Example coverage file |
| createExonDFBed | Function to create a list of exons from bed file of capture... |
| exonsTcellExTRECT | Function to run T cell ExTRECT and return data frame |
| exonwindowplot2 | Method for getting GC content in selected exons |
| GCcorrect | Method for correcting for GC biases |
| getCovFromBam | Function to create TCRA coverage file from bams |
| getLogRdf | Method for calculating log ratio from single region |
| getVDJFraction | Method for calculating final VDJ fraction |
| loadCov | Function to load coverage from getCovFromBam |
| medianExonCoverage | Calculate median values of coverage within exons in rolling... |
| medianFilter | Method for creating running medians |
| pipe | Pipe operator |
| plotTcellExTRECT | Function to plot output from T cell ExTRECT |
| runTcellExTRECT | Function to run T cell ExTRECT |
| slidingwindowplot_alt | Method for getting GC content in different window sizes |
| TCRA_exons_agilent_v2_hg19 | TCRA exons (hg19) |
| TCRA_exons_agilent_v2_hg38 | TCRA exons (hg38) |
| TCRA_exons_hg19 | TCRA exons (hg19) |
| TCRA_exons_hg38 | TCRA exons (hg38) |
| TCRA_exons_nimblegen_hg19 | TCRA exons from Nimblegen... |
| TCRA_exons_nimblegen_hg38 | TCRA exons from Nimblegen... |
| TCRA_fasta | TCRA fasta file |
| tcra_seg_hg19 | TCRA segments file (hg19) |
| tcra_seg_hg38 | TCRA segments file (hg38) |
| TCRA_segments | TCRA segments |
