This repository contains the scripts used to analyze our samples from treatment of PI3Kδi AMG319 in patients with resectable head and neck cancer in a neoadjuvant, double-blind, placebo-controlled randomised phase-II trial. The data contains single-cell Smart-seq2 and 10x samples.
This project requires the following modules/programs:
- TopHat (v1.4.1)
- HTSeq (v0.7.1)
- Cutadapt (v1.3)
- DESeq2 (v.1.14.1)
- fastcluster (v.1.1.25)
- dendextend (v.1.7.0)
- Cell Ranger (v2.0.2)
- Seurat (v2.1)
- MAST (1.8.2)
- You can follow the instructions for our mapping pipeline using Cell Ranger.
- For the single-cell quality control just pull our in-house script.
- Clustering of single-cell data with our pipeline using Seurat.
- You can pull our in-house pipeline for mapping bulk data.
Demultiplexing libraries: Cell Ranger was used to demultiplex the 10x libraries. And our in-house mapping pipeline was used for the bulk data.
Quality control: An in-house script was used to explore the quality of the data and select the thresholds.
Clustering: Seurat was used to cluster the data.
For more specific information about the data generation and processing, please check the methods.
Current maintainers:
- Ciro Ramírez-Suástegui (ksuasteguic@gmail.com, ciro@lji.org)
Please email Ciro Ramírez-Suástegui (ciro@lji.org) and Vijayanand Pandurangan (vijay@lji.org).