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AGFusion: annotate and visualize gene fusions

https://doi.org/10.1101/080903
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.ymeth.2012.09.013openalex-snapshot
Detecting and visualizing gene fusions
inferredcites →https://doi.org/10.1038/nbt.1754openalex-snapshot
Integrative genomics viewer
inferredcites →https://doi.org/10.1038/onc.2014.406openalex-snapshot
The landscape and therapeutic relevance of cancer-associated transcript fusions
inferredcites →https://doi.org/10.1093/bioinformatics/btt252openalex-snapshot
iFUSE: integrated fusion gene explorer
inferredcites →https://doi.org/10.1093/database/bar030openalex-snapshot
Ensembl BioMarts: a hub for data retrieval across taxonomic space
inferredcites →https://doi.org/10.1093/nar/gkv1157openalex-snapshot
Ensembl 2016
inferredcites →https://doi.org/10.1093/nar/gkv1344openalex-snapshot
The Pfam protein families database: towards a more sustainable future
inferredcites →https://doi.org/10.1101/gr.133744.111openalex-snapshot
Detecting differential usage of exons from RNA-seq data
inferredcites →https://doi.org/10.1158/2159-8290.cd-13-0050openalex-snapshot
Identification of Targetable FGFR Gene Fusions in Diverse Cancers
inferredcites →https://doi.org/10.1186/1471-2105-14-244openalex-snapshot
RCircos: an R package for Circos 2D track plots
inferredcites →https://doi.org/10.1186/s12918-014-0097-zopenalex-snapshot
Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/cam4.4943openalex-snapshot
Oncogenic fusion transcript analysis identified ADAP1‐NOC4L, potentially associated with metastatic colorectal cancer
inferred← citeshttps://doi.org/10.1007/978-1-0716-4734-9_17openalex-snapshot
Computational Methods for Cancer Neoantigen Prediction
inferred← citeshttps://doi.org/10.1007/s12672-024-01571-3openalex-snapshot
Identification of BRCA new prognostic targets and neoantigen candidates from fusion genes
inferred← citeshttps://doi.org/10.1016/j.cell.2023.07.014openalex-snapshot
Pan-cancer proteogenomics connects oncogenic drivers to functional states
inferred← citeshttps://doi.org/10.1016/j.celrep.2018.03.050openalex-snapshot
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers
inferred← citeshttps://doi.org/10.1016/j.semcancer.2021.07.003openalex-snapshot
Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology
inferred← citeshttps://doi.org/10.1016/j.tranon.2020.100884openalex-snapshot
RNA-sequencing of IDH-wild-type glioblastoma with chromothripsis identifies novel gene fusions with potential oncogenic properties
inferred← citeshttps://doi.org/10.1016/j.tranon.2020.100944openalex-snapshot
Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology
inferred← citeshttps://doi.org/10.1038/s10038-019-0687-0openalex-snapshot
Visualization tools for human structural variations identified by whole-genome sequencing
inferred← citeshttps://doi.org/10.1038/s41467-020-16434-yopenalex-snapshot
Evolution and structure of clinically relevant gene fusions in multiple myeloma
inferred← citeshttps://doi.org/10.1038/s41467-021-26871-yopenalex-snapshot
Genetic fusions favor tumorigenesis through degron loss in oncogenes
inferred← citeshttps://doi.org/10.1038/s41597-020-00761-2openalex-snapshot
Mining potentially actionable kinase gene fusions in cancer cell lines with the KuNG FU database
inferred← citeshttps://doi.org/10.1093/bib/bbac261openalex-snapshot
Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization
inferred← citeshttps://doi.org/10.1093/bib/bbaf302openalex-snapshot
Computational methods and data resources for predicting tumor neoantigens
inferred← citeshttps://doi.org/10.1093/gpbjnl/qzaf001openalex-snapshot
Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources
inferred← citeshttps://doi.org/10.1093/jnen/nlae105openalex-snapshot
Detection of rare and novel gene fusions in patients with diffuse glioma: An institutional retrospective study
inferred← citeshttps://doi.org/10.1093/nar/gkaa364openalex-snapshot
FGviewer: an online visualization tool for functional features of human fusion genes
inferred← citeshttps://doi.org/10.1093/nar/gkaf078openalex-snapshot
FuSViz—visualization and interpretation of structural variation using cancer genomics and transcriptomics data
inferred← citeshttps://doi.org/10.1101/2023.06.07.23291117openalex-snapshot
The Metastatic Breast Cancer Project: leveraging patient-partnered research to expand the clinical and genomic landscape of metastatic breast cancer and accelerate discoveries
inferred← citeshttps://doi.org/10.1101/839738openalex-snapshot
annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions
inferred← citeshttps://doi.org/10.1158/2326-6066.cir-19-0401openalex-snapshot
pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens
inferred← citeshttps://doi.org/10.1186/s12859-019-3145-2openalex-snapshot
MoMI-G: modular multi-scale integrated genome graph browser
inferred← citeshttps://doi.org/10.1186/s12859-020-03922-7openalex-snapshot
annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions
inferred← citeshttps://doi.org/10.1186/s13073-019-0666-2openalex-snapshot
Best practices for bioinformatic characterization of neoantigens for clinical utility
inferred← citeshttps://doi.org/10.1186/s13073-022-01060-8openalex-snapshot
Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma
inferred← citeshttps://doi.org/10.1186/s13073-024-01363-yopenalex-snapshot
Identification of tumor rejection antigens and the immunologic landscape of medulloblastoma
inferred← citeshttps://doi.org/10.1200/go-24-00289openalex-snapshot
Deep Diving Into the Fusion Across Cancer Types in the Indian Population From Formalin-Fixed Paraffin-Embedded RNA-Exome Data: A Road to Discovering Novel Rearrangements With Clinical Relevance
inferred← citeshttps://doi.org/10.1371/journal.pone.0196588openalex-snapshot
FusionHub: A unified web platform for annotation and visualization of gene fusion events in human cancer
inferred← citeshttps://doi.org/10.3389/fimmu.2021.748820openalex-snapshot
Novel Tumor-Specific Antigens for Immunotherapy Identified From Multi-omics Profiling in Thymic Carcinomas
inferred← citeshttps://doi.org/10.3390/cancers13061343openalex-snapshot
The Fusion Gene Landscape in Taiwanese Patients with Non-Small Cell Lung Cancer
inferred← citeshttps://doi.org/10.3390/ijms231911624openalex-snapshot
Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction
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