ArticleBioinformatics (Oxford, England)2021
Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- Addition of SHR-1701 to first-line capecitabine and oxaliplatin (XELOX) plus bevacizumab for unresectable metastatic colorectal cancer.Signal transduction and targeted therapy · 2024Trial
- Integrative multi-omics profiling reveals distinct evolutionary and immunogenic features of brain oligometastasis in lung adenocarcinoma.Genome medicine · 2026Article
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- Proteogenomic Characterization Reveals Subtype-Specific Therapeutic Potential for HER2-Low Breast Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Somatic mutation profiles in aged military nuclear test veterans: A comparative whole-genome sequence study.PloS one · 2026Article
- Single-cell and spatial transcriptomic characterization of pulmonary pleomorphic carcinoma.Communications biology · 2025Article
- Single-cell copy number alteration signature analysis reveals masked patterns and potential biomarkers for cancer.Communications biology · 2025Article
- Synchronous endometrial/cervical and ovarian/fallopian tube carcinoma: a genome-wide mutation analysis.The journal of pathology. Clinical research · 2025Article
- Benchmarking copy number variation detection with low-coverage whole-genome sequencing.Briefings in bioinformatics · 2025Article
- Article
- Integrated proteogenomic characterization of ampullary adenocarcinoma.Cell discovery · 2025Article
- Proteogenomic Landscape of Breast Ductal Carcinoma Reveals Tumor Progression Characteristics and Therapeutic Targets.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Whole-Exome Sequencing and Experimental Validation Unveil the Roles of TMEM229A Q200del Mutation in Lung Adenocarcinoma.The clinical respiratory journal · 2024Article
- The genomic landscape of lung cancer in never-smokers from the Women's Health Initiative.JCI insight · 2024Article
- Unveiling divergent treatment prognoses in IDHwt-GBM subtypes through multiomics clustering: a swift dual MRI-mRNA model for precise subtype prediction.Journal of translational medicine · 2024Article
- Comprehensive genomic profiling of pulmonary spindle cell carcinoma using tissue and plasma samples: insights from a real-world cohort analysis.The journal of pathology. Clinical research · 2024Article
- Follicular lymphoma B cells exhibit heterogeneous transcriptional states with associated somatic alterations and tumor microenvironments.Cell reports. Medicine · 2024Article
- Proteogenomic Workflow for Characterization of Microphthalmia Transcription Factor (MiT) Family Translocation Renal Cell Carcinoma.Methods in molecular biology (Clifton, N.J.) · 2024Article
- ANOS1 accelerates the progression of esophageal cancer identified by multi-omic approaches.American journal of cancer research · 2024Article
- Genomic alterations in the stepwise progression from normal mucosa to metastasizing oral squamous cell carcinoma.Frontiers in oncology · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryMutational signatures are recurring DNA alteration patterns caused by distinct mutational events during the evolution of cancer. In recent years, several bioinformatics tools are available for mutational signature analysis. However, most of them focus on specific type of mutation or have limited scope of application. A pipeline tool for comprehensive mutational signature analysis is still lacking. Here we present Sigflow pipeline, which provides an one-stop solution for de novo signature extraction, reference signature fitting, signature stability analysis, sample clustering based on signature exposure in different types of genome DNA alterations including single base substitution, doublet base substitution, small insertion and deletion and copy number alteration. A Docker image is constructed to solve the complex and time-consuming installation issues, and this enables reproducible research by version control of all dependent tools along with their environments. Sigflow pipeline can be applied to both human and mouse genomes. AVAILABILITY AND IMPLEMENTATION: Sigflow is an open source software under academic free license v3.0 and it is freely available at https://github.com/ShixiangWang/sigflow or https://hub.docker.com/r/shixiangwang/sigflow. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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