ArticleBioinformatics (Oxford, England)2022
hacksig: a unified and tidy R framework to easily compute gene expression signature scores.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Phase I/II Trial of Exportin 1 Inhibitor Selinexor plus Docetaxel in Previously Treated, Advanced KRAS-Mutant Non-Small Cell Lung Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Trial
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- Mechanistic dissection of GRHL2 and PR transcriptional co-regulation in breast cells.PLoS genetics · 2026Article
- The CXCL10/CXCR3 axis is essential for sustaining immunological dormancy in triple-negative breast cancer.NPJ breast cancer · 2026Article
- Caspase-2 deficiency drives pathogenic liver polyploidy and increases age-associated hepatocellular carcinoma in mice.Science advances · 2026Article
- Unraveling the YAP1-TGFβ1 axis: a key driver of androgen receptor loss in prostate cancer-associated fibroblasts.Journal of experimental & clinical cancer research : CR · 2025Article
- Cellular states associated with metastatic organotropism and survival in patients with pancreatic ductal adenocarcinoma.Nature genetics · 2025Article
- Personalized treatment in HPV+ oropharynx cancer using genomic adjusted radiation dose.The Journal of clinical investigation · 2025Observational
- CINSARC and Sarculator in Patients with Primary Retroperitoneal Sarcoma: A Combined Analysis of Single-Institution Data and the EORTC-STBSG-62092 Trial (STRASS).Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Article
- HPV16-Expressing Tumors Release Multiple IL1 Ligands to Orchestrate Systemic Immunosuppression Whose Disruption Enables Efficacy of a Therapeutic Vaccine.Cancer discovery · 2025Article
- Personalization of Radiotherapy Dose in HPV Positive Oropharynx Cancer Using GARD.medRxiv : the preprint server for health sciences · 2025Article
- Ferroptosis-Related Gene Signatures: Prognostic Role in HPV-Positive Oropharyngeal Squamous Cell Carcinoma.Cancers · 2025Article
- Optimised dissociation and multimodal profiling of prostate cancer stroma reveal fibromuscular cell heterogeneity with clinical correlates.Frontiers in cell and developmental biology · 2025Article
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- Peritoneal Microenvironment Promotes Appendiceal Adenocarcinoma Growth: A Multi-omics Approach Using Patient-Derived Xenografts.Molecular cancer research : MCR · 2024Article
- Androgen deprivation induces double-null prostate cancer via aberrant nuclear export and ribosomal biogenesis through HGF and Wnt activation.Nature communications · 2024Article
- An immuno-score signature of tumor immune microenvironment predicts clinical outcomes in locally advanced rectal cancer.Frontiers in oncology · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryHundreds of gene expression signatures have been developed during the last two decades. However, due to the multitude of development procedures and sometimes a lack of explanation for their implementation, it can become challenging to apply the original method on custom data. Moreover, at present, there is no unified and tidy interface to compute signature scores with different single sample enrichment methods. For these reasons, we developed hacksig, an R package intended as a unified framework to obtain single sample scores with a tidy output as well as a collection of manually curated gene signatures and methods from cancer transcriptomics literature. AVAILABILITY AND IMPLEMENTATION: The hacksig R package is freely available on CRAN (https://CRAN.R-project.org/package=hacksig) under the MIT license. The source code can be found on GitHub at https://github.com/Acare/hacksig. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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