Tcr/Bcr Receptor Utilities for Solid Tumors
TRUST extracts T/B cell receptor hypervariable CDR3 sequences from unselected tumor RNA-seq data. It is an ultra-sensitive de novo assembly method for calling CDR3s (Li et al., Nature Genetics, 2017), with demonstrated utilities when applied to large cancer genomics data (Li et al., Nature Genetics, 2016). It is written in Python2, with continued updates for performance improvements and additional functionalities. Currently, TRUST supports multiple RNA-seq aligners including Bowtie2, STAR, MapSplice2 etc. It also applies to both hg19 and hg38 human genome references. TRUST can run in parallel mode and uses GPU acceleration to increase computational efficiency. The source code, installation instructions, usage and related dataset are available at: bitbucket.org/liulab/trust/.
Tumor IMmune Estimation Resource
TIMER originally refers to the statistical deconvolution method we developed to estimate six different immune cell types in the tumor microenvironment using gene expression data (Li et al., Genome Biology, 2016). With that work, we published the first TIMER website (cistrome.org/TIMER), and kept a number of useful resources, including tumor purity estimation for over 9,000 TCGA tumors. Later on, we developed an interactive website where users are allowed to perform a number of analysis using the immune infiltration levels we estimated (Li T et al., Cancer Research, 2017), and published the current new website (https://cistrome.shinyapps.io/timer/). Questions can be addressed to Taiwen Li (firstname.lastname@example.org).
Clonal Heterogeneity Analysis Tool
CHAT is a collection of tools for studying intra-tumor heterogeneity using genomics data. The work of CHAT started when we developed a tumor purity inference algorithm (Li et al., Clinical Cancer Research, 2012) and revisited GBM classification. Modifications were made to the framework of this algorithm to allow the inference of the subclonality fractions (sAGP) of tumor somatic copy number alterations. Integrative analysis of sCNA data with whole exome sequencing data enabled the estimation of cancer cell fraction (CCF) of the somatic mutations. The temporal order for a pair of somatic events was also estimated when available (Li et al., Genome Biology, 2014). CHAT is available as an R package, and is also accessible from https://sourceforge.net/projects/clonalhetanalysistool/.