Deconvolving clinically relevant cellular immune crosstalk from bulk gene expression using CODEFACS and LIRICS stratifies melanoma patients to anti-PD-1 therapy
Creators
- 1. Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD
- 2. Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD; Department of Computer Science, University of Maryland, College Park, MD
- 3. Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD; Department of Artificial Intelligence & Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Suwon, Republic of Korea
- 4. Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD
Description
All the processed data and codes from the manuscript "Deconvolving clinically relevant cellular immune crosstalk from bulk gene expression using CODEFACS and LIRICS stratifies melanoma patients to anti-PD-1 therapy" are deposited here:
1. Eestimated cell fractions across 21 cancer types in TCGA:
cell_frac_TCGA.zip
2. List of cell fraction file names:
cell_frac_TCGA_files.txt
3. The primary tissue/cancer type names of processed TCGA data:
tumor_type_TCGA_deconv.txt
4. Deconvolved cell type specific expression for each sample across 21 cancer types in TCGA:
“CANCER TYPE/TISSUE TYPE.rds” e.g. melanoma.rds and breast.rds etc.
To merge all the datasets across 21 cancer types as a single RData file, you can run the code "merge_TCGA_deconvolved_data.r".
5. Curated benchmark datasets:
benchmark_datasets.RData
6. Performance of CODEFACS on benchmark datasets:
acc_benchmark_codefacs_12.20.RData and pred_benchmark_codefacs_12.20.RData
7. Estimated mean gene expression in each cell type based on publicly available single cell datasets across cancer types:
sc_mean_datasets.RData
8. The three Deconvolved ICB datasets (Riaz N. et al, Cell 2017, Gide T. et al, Cancer Cell 2019 and Liu D. et al, Nature Medicine 2019):
pred_ICB_codefacs_rsem.RData
9. Compressed signatures files for SKCM, GBM and NSCLC:
signature_files.zip
10. Data for supplementary figure S12, S13, S14, S15, S16, S30 and S34:
data_S12.S13.zip, data_simulated_sc_S14.S15.S16.zip, dat_stages_conf, coff_gene_gene_correlation_skcm.rds, coff_gene_gene_correlation_gbm.rds and coff_gene_gene_correlation_nsclc.rds
11. Gene list file:
gene_name_livnat.txt
12. All the relevant codes, scripts and curated database for CODEFACS and LIRICS:
CODEFACS&LIRICS-master.zip
Files
Restricted
The record is publicly accessible, but files are restricted to users with access.
Request access
If you would like to request access to these files, please fill out the form below.
You need to satisfy these conditions in order for this request to be accepted:
The source code is available for non-profit, academic research purposes only. Following the policy of NIH/NCI, the requesters should fill in, sign, and return the following software use agreement. The Recipient Investigator is most likely not the Authorized Recipient Official. An Authorized Recipient Official is someone who is authorized to sign legal documents on behalf of the institution; this person usually works in the Technology Transfer Department or the Office of Sponsored Research. The Authorized Recipient Official’s signature is legally binding upon the institution and they regularly sign contracts or research agreements. This software use agreement may also require review from your institution’s legal team.
We recommend the requesters to copy the following contents into a word processor, insert the specific research question to be addressed with the CODEFACS and LIRICS code, generate a PDF document with the requester's requisite signatures, and send it to Kevin Chang (changke@mail.nih.gov) along with Zenodo request. (Unfortunately, Zenodo does not have the option for us to provide the requesters with a Word document version of the software use agreement). If you have any questions, feel free to contact us.
====================================================================================================
SOFTWARE TRANSFER AGREEMENT
PROVIDER: National Cancer Institute (NCI)
RECIPIENT: _________________________________________
WHEREAS, PROVIDER has certain proprietary software and associated material described below
(hereinafter, collectively referred to as “Software”)
National Cancer Institute COnfident DEconvolution For All Cell Subsets (CODEFACS) and Ligand Receptor Interactions between Cell Subsets (LIRICS) software (NIH Ref. No. E-044-2020), provided as source codes (written in R) for two computer programs, i) CODEFACS: which estimates both cell type abundance and mean cell type gene expression levels in each sample and ii) LIRICS: which predicts ligand-receptor interactions that are likely to occur in specific patient sub-populations based on deconvolved expression from CODEFACS and a literature curated immunological database included within, as described in Wang, Patkar et al. (Cancer Discovery 2022, DOI: 10.1158/2159-8290.CD-21-0887), including further improvements thereof, and related documentation.
PROVIDER agrees to transfer such Software to RECIPIENT, to be used solely in connection
with the following research activity and for the following reasons (hereinafter “Project”). Describe
with specificity the scope of use of Software under this Agreement:
_____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________
NOW, THEREFORE, in consideration of the premises and mutual covenants contained herein, the
PROVIDER and RECIPIENT agree, and RECIPIENT SCIENTIST acknowledges as follows:
1. SOFTWARE SHALL NOT BE USED FOR TREATING OR DIAGNOSING HUMAN
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