This repository contains quality control, analysis script and supplementary tables for
Pernas et al 2022. Early on-treatment transcriptional profiling as a tool for improving response prediction in HER2-positive inflammatory breast cancer
manuscript.

The location of the raw data files on the O2 cluster: /n/data1/cores/bcbio/PIs/beth_overmoyer/overmoyer2021_RNAseq_analysis_of_inflammatory_breast_cancer_hbc04141/data/03_fastq/bovermoyer.tar - downloaded from the cloud.

Scripts:

• 01.get_data.sh - download input data from the cloud
• 02.untar.sh - unpack the input archive
• bcbio_config - configuration file for bcbio-nextgen RNA-seq pipeline
• 03.quality_control_se.Rmd - quality control script, the report was generated for 20 cases and for 22 cases (the main analysis is for 22 cases, the status of 2 cases was confirmed). pdf and html files are respective compiled reports.
• 04.de_workflow_day1.Rmd - differential expression workflow for day1 samples
• 04.de_workflow_day8.Rmd - differential expresison workflow for day8 samples
• 04.de_workflow.Rmd - differential expression workflow for all samples pdf and html files are respective compiled reports.
• 04.de_workflow.paired.Rmd - paired differential expression workflow (the above scripts were unpaired analyses) 04.de_workflow.pdf
• 05.functional_analysis.Rmd - functional analysis workflow. The main gene enrichment analysis was performed in GSEA, see supplementary tables.
• 06.fardeep.Rmd - farDEEP workflow - cell type deconvolution analysis
• 07.fig3.R - a script generating fig3
• 08.fig4.R - a script generating fig4
• overmoyer2021.paired_test.xlsx - paired DE analysis result
• overmoyer2021.xlsx - supplementary tables