inst/markdown/methods/TCR.markdown

In CRI-iAtlas/iatlas-app: What the Package Does (One Line, Title Case)

Title: TCR Inference from Tumor RNA-Seq Data

Descriptions: Identification of TCR CDR3 sequences from T cells present in the sequenced tumor sections was performed using MiTCR v1.0.3,(Bolotin et al., 2013) and previously described parameters to optimize extraction from RNA-seq datasets (Brown et al., 2015). Briefly, paired-end fastq files were concatenated into a single file and run through MiTCR using the appropriate parameter set for the sequence read length as described in Brown et al. Runs were performed on the ISB Cancer Genomics Cloud. TCR diversity scores (Shannon Entropy, Evenness, and Richness) are provided in manuscript Table S1 and in this tool.

Reference List

Contributors: Scott D. Brown, Sheila M. Reynolds

CRI-iAtlas/iatlas-app documentation built on Feb. 7, 2025, 9:02 p.m.