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2. Community-driven ELIXIR activities in single-cell omics [version 1; peer review: awaiting peer review]

4. Interactive visualization as a key tool for understanding medical omics data

5. Tximeta: Reference sequence checksums for provenance identification in RNA-seq

6. O-0025COLORECTAL CANCER SUBTYPING CONSORTIUM (CRCSC) IDENTIFIES CONSENSUS OF MOLECULAR SUBTYPES

8. The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

9. Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage.

10. A glioma classification scheme based on coexpression modules of EGFR and PDGFRA

11. Colorectal Cancer Subtyping Consortium (CRCSC) Identifies Consensus of Molecular Subtypes

16. O-0025COLORECTAL CANCER SUBTYPING CONSORTIUM (CRCSC) IDENTIFIES CONSENSUS OF MOLECULAR SUBTYPES

17. The projection score - an evaluation criterion for variable subset selection in PCA visualization

18. Integrative analysis of gene expression and copy number alterations using canonical correlation analysis

19. Deep quantification of substrate turnover defines protease subsite cooperativity.

20. DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes.

22. The tidyomics ecosystem: enhancing omic data analyses.

23. Rbm8a deficiency causes hematopoietic defects by modulating Wnt/PCP signaling.

24. Convergence of multiple RNA-silencing pathways on GW182/TNRC6.

25. Conserved stromal-immune cell circuits secure B cell homeostasis and function.

26. mutscan-a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data.

27. Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.

28. The shaky foundations of simulating single-cell RNA sequencing data.

29. Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencing.

30. A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data.

31. monaLisa: an R/Bioconductor package for identifying regulatory motifs.

32. Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma.

33. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data.

34. Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines.

35. treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses.

36. CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data.

37. A unique bipartite Polycomb signature regulates stimulus-response transcription during development.

38. Preprocessing choices affect RNA velocity results for droplet scRNA-seq data.

39. MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome.

40. muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data.

41. TreeSummarizedExperiment: a S4 class for data with hierarchical structure.

42. Alignment and mapping methodology influence transcript abundance estimation.

43. ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R.

44. Tximeta: Reference sequence checksums for provenance identification in RNA-seq.

45. Orchestrating single-cell analysis with Bioconductor.

47. HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats.

48. A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes.

49. ARMOR: An A utomated R eproducible MO dular Workflow for Preprocessing and Differential Analysis of R NA-seq Data.

50. Essential guidelines for computational method benchmarking.

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