gene set analysis Multi-omics integration single sample tumor subtype Increasing numbers of studies report comprehensive molecular profiling using multiple different experimental approaches on the same set of biological samples. These multi-omics studies can potentially yield great insights into the complex ...
A multivariate approach to the integration of multi-omics datasets. BMC Bioinformatics. 2014. doi:10.1186/1471-2105-15-162. Google Scholar Meng C. omicade4 R package. Bioconductor 3.3; https://www.bioconductor.org/packages/release/bioc/html/omicade4.html. Louhimo R, Hautaniemi S. CNAmet...
Figure 1. Integration of LIANA and Tensor-cell2cell to identify context-driven programs of cell-cell communication LIANA and Tensor-cell2cell can be used together to infer the molecular basis of cell-cell interactions by running analysis across multiple samples, conditions, or contexts. Given a ...
Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials. Nat. Biotechnol. 42, 1133–1149 (2023). Article PubMed PubMed Central MATH Google Scholar Collins, B. C. et al. Multi-laboratory assessment of reproducibility, qualitative and quantitative ...
The integrated analysis of multiple gene expression profiles previously measured in distinct studies is problematic since missing both sample matches and common labels prevent their integration in fully data-driven, unsupervised training. In this study, we propose a strategy to enable the integration of...
Single-cell multi-omics Multi-omics single-cell methods interrogate multiple levels of molecular information from a single cell, such as DNA & RNA, RNA & protein, or three layers combined [126]. By combining these methods, it is feasible to gain deeper insight into genotype-phenotype relationshi...
Several systematic prediction models for drug selection in cancer exist, in which omics data are leveraged to determine the chemotherapies’ “killing potential” of tumour cells [8,9,10,11]. However, these models are not immediately translatable to IMIDs as they are (1) trained on large publi...
Seurat v4.1.1 was used for mapping of obtained T-cell transcriptomes following the steps detailed in the author’s tutorial [48]. Mapping anchors were identified using the function FindIntegrationAnchors with k.filter = 100, dims = 1:10, and reference.reduction = “pca” (as ...
which is reported to be enough to obtain converged binding energy values. The absolute binding free energy was calculated using four efficient methods: thermodynamic integration (TI), free energy perturbation (FEP), quadrature-based integration of TI, and Bennett’s acceptance ratio (BAR) method. ...
Multidimensional approaches for studying plant defence against insects: From ecology to omics and synthetic biology. J. Exp. Bot. 2015, 66, 479–493. [Google Scholar] [CrossRef] [Green Version] Chakradhar, T.; Hindu, V.; Reddy, P.S. Genomic-based-breeding tools for tropical maize ...