Conserved programs and specificities of T cells targeting hematological malignancies: single cell and TCR data analysis repository

README Repository for "Conserved programs and specificities of T cells targeting hematological malignancies" This repository hosts the data and analysis scripts associated with the research paper "Conserved programs and specificities of T cells targeting hematological malignancies." It provides comprehensive resources for understanding the computational analyses underpinning the study's findings, focusing on the identification and characterization of tumor-reactive T-cell receptor (TCR) sequences and their associated molecular signatures in multiple myeloma (MM) and acute myeloid leukemia (AML). Analysis Overview The analysis encompasses comprehensive processing and integration of: Single-cell RNA sequencing (scRNA-seq) data from 20 patients (20 MM) AML: Single-cell RNA sequencing and VDJ sequencing from 10.1038/s41467-021-26282-z Single-cell V(D)J sequencing (scVDJ-seq) for TCR identification Longitudinal clinical trial datasets for therapeutic response analysis Directory Structure data_objects/ - Contains processed Seurat objects and TCR datasets with patient-identifying information removed for privacy data_processing/ - Scripts for quality control and pre-processing of single-cell RNA-seq and TCR data Main packages used: Seurat, tidyverse, Cell Ranger TCR_analysis/ - Scripts for TCR clonotype identification, similarity analysis, and convergent sequence detection Main packages used: tidyverse, msa, turbogliph, ggraph, igraph single_cell_analysis/ - Scripts for scRNA-seq analysis, TFiT signature development, and transcriptional state characterization Main packages used: Seurat, AUCell, Harmony, presto, ggplot2 extended_analysis/ - Scripts for validation in additional cohorts (clinical trials, AML checkpoint inhibitor datasets) Dependencies Major R packages required: Seurat (≥5.0.1) tidyverse AUCell (≥1.24.0) Harmony (≥0.1.1) presto (≥1.0.0) msa turbogliph