Software

See also my profile on Forge INRAE or on Github for more (including code snippet).

• Software, as maintainer
• Software, as author
• Websites
• Datasets

Software, as maintainer

1. Vialaneix, N., Picheny, V., & Servien, R. (2026). SISIR: Select Intervals Suited for Functional Regression. R package version 0.2.5 (2026-07-02), published on CRAN. Maintainer
   
   Bib Entry

   • @manual{vialaneix_etal_SISIR,
       title = {{SISIR}: Select Intervals Suited for Functional Regression},
       author = {Vialaneix, Nathalie and Picheny, Victor and Servien, R\'emi},
       year = {2026},
       howpublished = {R package version 0.2.5 (2026-07-02), published on CRAN},
       keywords = {moi, software},
       owner = {nathalie},
       status = {softmain},
       timestamp = {2016.12.11},
       url = {http://CRAN.R-project.org/package=SISIR},
       webnote = {Maintainer}
     }
     

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2. Vialaneix, N., Cardenas, G., Chavent, M., Foissac, S., Neuvial, P., & Randriamihamison, N. ëlle. (2026). treediff: Testing Differences Between Families of Trees. R package version 0.2.3 (2026-06-08), published on CRAN. Maintainer
   
   Bib Entry

   • @manual{vialaneix_etal_treediff,
       title = {{treediff}: Testing Differences Between Families of Trees},
       author = {Vialaneix, Nathalie and Cardenas, Gwenda\"elle and Chavent, Marie and Foissac, Sylvain and Neuvial, Pierre and Randriamihamison, Nathana \"elle},
       year = {2026},
       howpublished = {R package version 0.2.3 (2026-06-08), published on CRAN},
       keywords = {software, moi},
       owner = {nathalie},
       status = {softmain},
       timestamp = {2026.08.23},
       url = {https://cran.r-project.org/package=treediff},
       webnote = {Maintainer}
     }
     

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3. Mariette, J., Brouard, C., Flamary, R., & Vialaneix, N. (2025). mixKernel: Omics Data Integration Using Kernel Methods. R package version 0.9-2 (2025-04-19), published on CRAN. Maintainer
   
   Bib Entry

   • @manual{mariette_vialaneix_mixKernel,
       title = {{mixKernel}: Omics Data Integration Using Kernel Methods},
       author = {Mariette, J\'er\^ome and Brouard, C\'eline and Flamary, R\'emi and Vialaneix, Nathalie},
       year = {2025},
       howpublished = {R package version 0.9-2 (2025-04-19), published on CRAN},
       keywords = {moi, software},
       owner = {nathalie},
       status = {softmain},
       timestamp = {2017.07.19},
       url = {http://CRAN.R-project.org/package=mixKernel},
       webnote = {Maintainer}
     }
     

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4. Vialaneix, N., Maigné, É., Mariette, J., Olteanu, M., Rossi, F., Bendhaïba, L., & Boelaërt, J. (2025). SOMbrero: SOM Bound to Realize Euclidean and Relational Outputs. R package (CRAN), R package version 1.5.0 (2025-10-06). Maintainer
   
   Bib Entry

   • @manual{vialaneix_etal_SOMB,
       title = {{SOMbrero}: SOM Bound to Realize Euclidean and Relational Outputs},
       author = {Vialaneix, Nathalie and Maign\'e, \'Elise and Mariette, J\'erome and Olteanu, Madalina and Rossi, Fabrice and Bendha\"iba, Laura and Boela\"ert, Julien},
       year = {2025},
       note = {R package version 1.5.0 (2025-10-06)},
       howpublished = {R package (CRAN)},
       keywords = {moi, software},
       owner = {nathalie},
       status = {softmain},
       timestamp = {2014.05.21},
       url = {http://CRAN.R-project.org/package=SOMbrero},
       webnote = {Maintainer}
     }
     

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5. Vialaneix, N., & Imbert, A. (2024). RNAseqNet: Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation. R package version 0.1.5 (2024-02-20), published on CRAN. Maintainer
   
   Bib Entry

   • @manual{vialaneix_imbert_RNAseqNet,
       title = {{RNAseqNet}: Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation},
       author = {Vialaneix, Nathalie and Imbert, Alyssa},
       year = {2024},
       howpublished = {R package version 0.1.5 (2024-02-20), published on CRAN},
       keywords = {moi, software},
       owner = {nathalie},
       status = {softmain},
       timestamp = {2017.07.19},
       url = {http://CRAN.R-project.org/package=RNAseqNet},
       webnote = {Maintainer}
     }
     

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Software, as author

1. Servien, R., Guilmineau, C., & Vialaneix, N. (2026). phoenics: Pathways Longitudinal and Differential Analysis in Metabolomics. R package version 0.6.1 (2026-07-02), published on CRAN.
   
   Bib Entry

   • @manual{servien_etal_phoenics,
       title = {{phoenics}: Pathways Longitudinal and Differential Analysis in Metabolomics},
       author = {Servien, R\'emi and Guilmineau, Camille and Vialaneix, Nathalie},
       year = {2026},
       howpublished = {R package version 0.6.1 (2026-07-02), published on CRAN},
       keywords = {moi, software},
       owner = {nathalie},
       status = {softauth},
       timestamp = {2026.05.30},
       url = {http://CRAN.R-project.org/package=phoenics}
     }
     

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2. Maigné, É., Noirot, C., Henry, J., Adu Kesewaah, Y., Badin, L., Déjean, S., Guilmineau, C., Krebs, A., Mathevet, F., Segalini, A., Thomassin, L., Colongo, D., Gaspin, C., Liaubet, L., & Vialaneix, N. (2026). ASTERICS: A Tool for the ExploRation and Integration of omiCS data. Current version: 5.0.
   
   Bib Entry

   • @manual{maigne_etal_ASTERICS,
       title = {{ASTERICS}: {A} {T}ool for the {E}xplo{R}ation and {I}ntegration of omi{CS} data},
       author = {Maign\'e, \'Elise and Noirot, C\'eline and Henry, Julien and Adu Kesewaah, Yaa and Badin, Ludovic and D\'ejean, S\'ebastien and Guilmineau, Camille and Krebs, Arielle and Mathevet, Fanny and Segalini, Audrey and Thomassin, Laurent and Colongo, David and Gaspin, Christine and Liaubet, Laurence and Vialaneix, Nathalie},
       year = {2026},
       note = {Current version: 5.0},
       keywords = {moi, software},
       owner = {nathalie},
       status = {softauth},
       timestamp = {2023.03.15},
       url = {https://asterics.miat.inrae.fr}
     }
     

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3. Jorge, E., Hocking, T., Neuvial, P., Vialaneix, N., & Foissac, S. (2026). hicream: HIC diffeREntial Analysis Method. R package version 0.0.4 (2026-01-30), published on CRAN.
   
   Bib Entry

   • @manual{jorge_etal_hicream2026,
       title = {hicream: HIC diffeREntial Analysis Method},
       author = {Jorge, Elise and Hocking, Toby and Neuvial, Pierre and Vialaneix, Nathalie and Foissac, Sylvain},
       year = {2026},
       howpublished = {R package version 0.0.4 (2026-01-30), published on CRAN},
       keywords = {moi, software},
       owner = {nathalie},
       status = {softauth},
       timestamp = {2018.07.25},
       url = {https://bioconductor.org/packages/ASICS/}
     }
     

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4. Neuvial, P., Ambroise, C., Chaturvedi, S., Dehman, A., Koskas, M., Rigaill, G., Vialaneix, N., & Hoffman, G. (2025). adjclust: Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix. R package version 0.6.11 (2025-11-20), published on CRAN.
   
   Bib Entry

   • @manual{neuvial_etal_adjclust,
       title = {adjclust: Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix},
       author = {Neuvial, Pierre and Ambroise, Christophe and Chaturvedi, Shubham and Dehman, Alia and Koskas, Michel and Rigaill, Guillem and Vialaneix, Nathalie and Hoffman, Gabriel},
       year = {2025},
       howpublished = {R package version 0.6.11 (2025-11-20), published on CRAN},
       keywords = {moi, software},
       owner = {nathalie},
       status = {softauth},
       timestamp = {2018.07.25},
       url = {http://CRAN.R-project.org/package=adjclust}
     }
     

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5. Lefort, G., Servien, R., Tardivel, P., & Villa-Vialaneix, N. (2020). ASICS: Automatic Statistical Identification in Complex Spectra. R package version 2.4.0 (2020-04-28), published on Bioconductor.
   
   Bib Entry

   • @manual{lefort_etal_ASICS,
       title = {ASICS: Automatic Statistical Identification in Complex Spectra},
       author = {Lefort, Ga\"elle and Servien, R\'emi and Tardivel, Patrick and Villa-Vialaneix, Nathalie},
       year = {2020},
       note = {R package version 2.4.0 (2020-04-28), published on Bioconductor},
       keywords = {moi, software},
       owner = {nathalie},
       status = {softauth},
       timestamp = {2018.07.25},
       url = {https://bioconductor.org/packages/ASICS/}
     }
     

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6. Lefort, G., Servien, R., Tardivel, P., & Villa-Vialaneix, N. (2020). ASICSdata: Example of 1D NMR spectra data for ASICS package. R package version 1.0.0 (2020-05-07), published on Biocondutor (data package).
   
   Bib Entry

   • @manual{lefort_etal_ASICSdata2018,
       title = {ASICSdata: Example of 1D NMR spectra data for ASICS package},
       author = {Lefort, Ga\"elle and Servien, R\'emi and Tardivel, Patrick and Villa-Vialaneix, Nathalie},
       year = {2020},
       note = {R package version 1.0.0 (2020-05-07), published on Biocondutor (data package)},
       keywords = {moi, data, software},
       owner = {nathalie},
       status = {softauth},
       timestamp = {2018.07.25},
       url = {https://bioconductor.org/packages/ASICSdata/}
     }
     

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Websites

1. Aubert, J., Hocking, T. D., & Vialaneix, N. (2023). CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics. CRAN, Ressource webpage.
   
   Bib Entry

   • @manual{aubert_etal_OmicsTV,
       title = {CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics},
       author = {Aubert, Julie and Hocking, Toby Dylan and Vialaneix, Nathalie},
       organization = {CRAN},
       year = {2023},
       note = {Ressource webpage},
       keywords = {moi, software},
       owner = {nathalie},
       status = {website},
       timestamp = {2023-07-17},
       url = {https://cran.r-project.org/web/views/Omics.html}
     }
     

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2. Josse, J., Mayer, I., Tierney, N., & Vialaneix, N. (2023). CRAN Task View: Missing Data. CRAN, Ressource webpage.
   
   Bib Entry

   • @manual{josse_etal_MissingDataTV,
       title = {CRAN Task View: Missing Data},
       author = {Josse, Julie and Mayer, Imke and Tierney, Nicholas and Vialaneix, Nathalie},
       organization = {CRAN},
       year = {2023},
       note = {Ressource webpage},
       keywords = {moi, software},
       owner = {nathalie},
       status = {website},
       timestamp = {2023-07-17},
       url = {https://cran.r-project.org/web/views/MissingData.html}
     }
     

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3. Josse, J., Mayer, I., Tierney, N., & Vialaneix, N. (2020). R-miss-tastic: A resource website on missing values - Methods and references for managing missing data. Ressource website.
   
   Bib Entry

   • @manual{josse_etal_RMT,
       title = {R-miss-tastic: A resource website on missing values - Methods and references for managing missing data},
       author = {Josse, Julie and Mayer, Imke and Tierney, Nicholas and Vialaneix, Nathalie},
       year = {2020},
       note = {Ressource website},
       keywords = {moi, software},
       owner = {nathalie},
       status = {website},
       timestamp = {2020-07-08},
       url = {https://rmisstastic.netlify.ap}
     }
     

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Datasets

1. Vialaneix, N., & Foissac, S. (2023). Genome 3D structure in pig fetal muscle from Hi-C assays of Chromatin Conformation Capture (Version V2.2). Recherche Data Gouv, Curator and contact.
   
   Bib Entry

   • @manual{vialaneix_foissac_8BLMNQ,
       title = {Genome 3D structure in pig fetal muscle from Hi-C assays of Chromatin Conformation Capture},
       author = {Vialaneix, Nathalie and Foissac, Sylvain},
       year = {2023},
       note = {Curator and contact},
       doi = {10.15454/8BLMNQ},
       keywords = {moi, data},
       owner = {nathalie},
       publisher = {Recherche Data Gouv},
       status = {data},
       timestamp = {2023.07.13},
       version = {V2.2}
     }
     

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2. Vialaneix, N., & Foissac, S. (2023). Companion dataverse for “Major reorganization of chromosome conformation during muscle development in pig” (Version V1.3). Recherche Data Gouv, Curator and contact.
   
   Bib Entry

   • @manual{foissac_vialaneix_DOMEHB,
       title = {Companion dataverse for ``{M}ajor reorganization of chromosome conformation during muscle development in pig''},
       author = {Vialaneix, Nathalie and Foissac, Sylvain},
       year = {2023},
       note = {Curator and contact},
       doi = {10.15454/DOMEHB},
       keywords = {moi, data},
       owner = {nathalie},
       publisher = {Recherche Data Gouv},
       status = {data},
       timestamp = {2023.07.13},
       version = {V1.3}
     }
     

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3. Vialaneix, N., & Liaubet, L. (2023). PigLet case study for ASTERICS (Version V1.2). Recherche Data Gouv, Curator and contact.
   
   Bib Entry

   • @manual{vialaneix_liaubet_TCKSTD,
       title = {{PigLet case study for ASTERICS}},
       author = {Vialaneix, Nathalie and Liaubet, Laurence},
       year = {2023},
       note = {Curator and contact},
       doi = {10.57745/TCKSTD},
       keywords = {moi, data},
       owner = {nathalie},
       publisher = {Recherche Data Gouv},
       status = {data},
       timestamp = {2023.07.13},
       version = {V1.2}
     }
     

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4. Brouard, C., Mourad, R., & Vialaneix, N. (2023). Expression + gene network datasets for benchmarking (Version V2.1). Recherche Data Gouv, Curator and contact.
   
   Bib Entry

   • @manual{brouard_etal_BZ0TTC,
       title = {{Expression + gene network datasets for benchmarking}},
       author = {Brouard, C\'eline and Mourad, Rapha\"el and Vialaneix, Nathalie},
       year = {2023},
       note = {Curator and contact},
       doi = {10.57745/BZ0TTC},
       keywords = {moi, data},
       owner = {nathalie},
       publisher = {Recherche Data Gouv},
       status = {data},
       timestamp = {2023.07.13},
       version = {V2.1}
     }
     

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5. Vialaneix, N., & Servien, R. (2023). Companion datasets for “A random forest approach for interval selection in functional regression” (Version V2.1). Recherche Data Gouv. Curator and contact
   
   Bib Entry

   • @manual{vialaneix_servien_KMH2GP,
       title = {{Companion datasets for ``A random forest approach for interval selection in functional regression''}},
       author = {Vialaneix, Nathalie and Servien, R\'emi},
       year = {2023},
       doi = {10.57745/KMH2GP},
       keywords = {moi, data},
       owner = {nathalie},
       publisher = {Recherche Data Gouv},
       status = {data},
       timestamp = {2023.07.21},
       version = {V2.1},
       webnote = {Curator and contact}
     }
     

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6. Vialaneix, N., Beaumont, M., & Malonga, T. (2023). single-cell RNA-seq of rabbit (Oryctolagus cuniculus) caecum epithelium (Version V1.0). Recherche Data Gouv, Curator and contact.
   
   Bib Entry

   • @manual{vialaneix_etal_0NUYZR,
       title = {single-cell {RNA-seq} of rabbit ({O}ryctolagus cuniculus) caecum epithelium},
       author = {Vialaneix, Nathalie and Beaumont, Martin and Malonga, Tania},
       year = {2023},
       note = {Curator and contact},
       doi = {10.57745/0NUYZR},
       keywords = {moi, data},
       owner = {nathalie},
       publisher = {Recherche Data Gouv},
       status = {data},
       timestamp = {2023.07.13},
       version = {V1.0}
     }
     

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7. Vialaneix, N. (2021). TCGA case study for ASTERICS (Version V3.0). Recherche Data Gouv, Curator and contact.
   
   Bib Entry

   • @manual{vialaneix_YNMQUY,
       title = {{TCGA case study for ASTERICS}},
       author = {Vialaneix, Nathalie},
       year = {2021},
       note = {Curator and contact},
       doi = {10.15454/YNMQUY},
       keywords = {moi, data},
       owner = {nathalie},
       publisher = {Recherche Data Gouv},
       status = {data},
       timestamp = {2023.07.13},
       version = {V3.0}
     }
     

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