Multi-omic data integration

  • padma: Pathway deviation scores using multiple factor analysis, available at BioC
  • Regeneration Rosetta: An R/Shiny interactive web application to explore regeneration-associated gene expression and chromatin accessibility, available as a Shiny web app
  • maskmeans: Multi-view aggregation/splitting K-means clustering algorithm, available at GitHub
  • Edge in TCGA: An R/Shiny interactive web application for the exploration of drivers of gene expression in The Cancer Genome Atlas, available as a Shiny web app

  • Rau, A., Manansala, R., Flister, M. J., Rui, H., Jaffrézic, F., Laloë, D., and Auer, P. L. (2020) Individualized multi-omic pathway deviation scores using multiple factor analysis. Biostatistics, kxaa029. HAL PDF Preprint Software Code
  • Godichon-Baggioni, A., Maugis-Rabusseau, C. and Rau, A. (2020) Multi-view cluster aggregation and splitting, with an application to multi-omic breast cancer data. Annals of Applied Statistics, 14:2, 752-767. HAL PDF Code
  • Foissac, S., Djebali, S., Munyard, K., Villa-Vialaneix, N., Rau, A., Muret, K., Esquerre, D., Zytnicki, M., Derrien, T., Bardou, P., Blanc, F., Cabau, C., Crisci, E., Dhorne-Pollet, S., Drouet, F., Gonzales, I., Goubil, A., Lacroix-Lamande, S., Laurent, F., Marthey, S., Marti-Marimon, M., Momal-Leisenring, R., Mompart, F., Quere, P., Robelin, D., San Cristobal, M., Tosser-Klopp, G., Vincent-Naulleau, S., Fabre, S., Pinard-Van der Laan, M.-H., Klopp, C., Tixier-Boichard, M., Acloque, H., Lagarrigue, S., Giuffra, E. (2019) Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biology, 18:48. HAL PDF Preprint Website
  • Dhara, S., Rau, A., Flister, M., Recka, N., Laiosa, M., Auer, P., and Udvadia, A. (2019) Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors. Scientific Reports, 9:14198. HAL PDF Preprint Code Shiny app
  • Rau, A., Dhara, S., Udvadia, A., and Auer, P. (2019) Regeneration Rosetta: An interactive web application to explore regeneration-associated gene expression and chromatin accessibility. G3: Genes|Genomes|Genetics, 9(12): 3953-3959. HAL PDF Code Shiny app
  • Rau, A., Flister, M. J., Rui, H. and Livermore Auer, P. (2019) Exploring drivers of gene expression in The Cancer Genome Atlas. Bioinformatics, 35(1): 62-68. HAL PDF Preprint Code Shiny app

Talks

Exploring drivers of gene expression in The Cancer Genome Atlas
Mar 28, 2018 8:30 AM
Exploring drivers of gene expression in The Cancer Genome Atlas
Dec 4, 2018 3:30 PM
Multi-omic integration for enhanced interpretability in exploratory analyses
Apr 29, 2021 2:00 PM