Ionizing Radiation Enhances Prognostically Significant Cellular Immunity Programs in the Brain Metastasis Microenvironment.
The 1 match · it ties a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
- [1] § Materials and Methods › Transcriptional expression analysis ↔ r/edger.R, the whole file · a weak match · score 0.60 · edgeR, featureCounts, filtered, CPM, Raw, TMM
Paper
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The authors' code
R · 41 lines · 1.5 KB · no license · 1 match
- # Load required packages
- library(edgeR)
- # Define file paths (consider making these command-line arguments)
- count_file <- "./featurecount_raw_counts.csv.gz"
- metadata_file <- "./sample_til_grade.csv.gz"
- output_file <- "./normalized_cts.csv"
- # Load and prepare count matrix
- cts <- read.csv("./featurecount_raw_counts.csv.gz",
- row.names = 1, # Use first column as row names directly
- check.names = FALSE,
- stringsAsFactors = FALSE)
- # Load and prepare sample metadata
- metadata <- read.csv("./sample_til_grade.csv.gz",
- stringsAsFactors = FALSE,
- check.names = FALSE)
- grade_mapping <- metadata$TIL.grade[match(colnames(cts), metadata$Sample.ID)]
- # Create data frame with proper names
- grade_df <- data.frame(sample_id = colnames(cts),
- grade = factor(grade_mapping),
- row.names = colnames(cts),
- stringsAsFactors = FALSE)
- # Normalize count data using edgeR's TMM method
- y <- DGEList(counts = cts,
- group = grade_df$grade,
- genes = rownames(cts))
- keep <- filterByExpr(y)
- cat(paste("Keeping", sum(keep), "of", length(keep), "genes after filtering\n"))
- y <- y[keep, , keep.lib.sizes = FALSE]
- y <- calcNormFactors(y, method = "TMM")
- normalized_cts <- cpm(y, log = TRUE, prior.count = 1)
- # Export normalized counts to file
- write.table(normalized.cts,
- "./normalized_cts.csv",
- row.names = FALSE,
- quote = FALSE)
edger.R at commit dfa58c1, no license · at the source
Overview
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, Texas
Abstract
The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.
Repository
Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.
JiangMDA/fukumura_ccr_2026
dfa58c19737181fad24f941345f43d4b390a4da5, 14 January 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
4 files
- r/
edger.R , R, 41 lines, 1 match - r/
estimate.R , R, 7 lines - r/
mcpcounter.R , R, 15 lines - README.md, Text, 1 line
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
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- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
Datasets cited
- bioproject:PRJNA1320836, at NCBI BioProject; found in “Data Availability”
Code and data availability statement
The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to a dataset: NCBI BioProject PRJNA1320836
- it points to the authors' code: JiangMDA/
fukumura_ccr_2026 - it says that the data are available on request
Read it in the paper: doi.org/10.1158/1078-0432.ccr-25-3525.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 2, 28 September 2026
- Publisher: n/a → American Association for Cancer Research
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 13 authors, 13 MeSH terms, 6 funders, 47 references, 6 RRIDs.
Cite
This paper
Fukumura, K., Jiang, P., Yeboa, D. N., Singareeka Raghavendra, A., Gubbiotti, M. A., Andersen, C. R., Ferguson, S. D., Duose, D. Y., Kudo, Y., Arun, B., Reuben, A., Huse, J. T., & Ibrahim, N. K. (2026). Ionizing Radiation Enhances Prognostically Significant Cellular Immunity Programs in the Brain Metastasis Microenvironment. Clinical cancer research : an official journal of the American Association for Cancer Research, 32(11), 2305-2316. https://
BibTeX
@article{fukumura2026ion
author = {Fukumura, Kazutaka and Jiang, Peixin and Yeboa, Debra Nana and Singareeka Raghavendra, Akshara and Gubbiotti, Maria A and Andersen, Clark R and Ferguson, Sherise D and Duose, Dzifa Yawa and Kudo, Yujin and Arun, Banu and Reuben, Alexandre and Huse, Jason T and Ibrahim, Nuhad K},
title = {{Ionizing Radiation Enhances Prognostically Significant Cellular Immunity Programs in the Brain Metastasis Microenvironment}},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
year = {2026},
month = jun,
volume = {32},
number = {11},
pages = {2305--2316},
publisher = {American Association for Cancer Research},
issn = {1078-0432},
doi = {10.1158/
url = {https://
pmid = {41817317},
pmcid = {PMC13223553}
}
RIS
TY - JOUR
AU - Fukumura, Kazutaka
AU - Jiang, Peixin
AU - Yeboa, Debra Nana
AU - Singareeka Raghavendra, Akshara
AU - Gubbiotti, Maria A
AU - Andersen, Clark R
AU - Ferguson, Sherise D
AU - Duose, Dzifa Yawa
AU - Kudo, Yujin
AU - Arun, Banu
AU - Reuben, Alexandre
AU - Huse, Jason T
AU - Ibrahim, Nuhad K
TI - Ionizing Radiation Enhances Prognostically Significant Cellular Immunity Programs in the Brain Metastasis Microenvironment
T2 - Clinical cancer research : an official journal of the American Association for Cancer Research
J2 - Clin Cancer Res
PY - 2026
DA - 2026/
VL - 32
IS - 11
SP - 2305
EP - 2316
SN - 1078-0432
PB - American Association for Cancer Research
DO - 10.1158/
UR - https://
LA - en
ER -
CSL-JSON
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"title": "Ionizing Radiation Enhances Prognostically Significant Cellular Immunity Programs in the Brain Metastasis Microenvironment",
"container-title": "Clinical cancer research : an official journal of the American Association for Cancer Research",
"author": [
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"container-title-short":
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"language": "en",
"issued": {
"date-parts": [
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