Methods

Survival analysis methods are often used in cancer studies. It has been shown that the combination of clinical data with genomics increases the predictive performance of survival analysis methods. But, this leads to a high-dimensional data problem. Fortunately, new methods ...

The aim of may RNA-seq studies is differential expression (DE) analysis between conditions of interest. The decreasing cost of sequencing has allowed for complex experimental designs, involving many samples over multiple conditions. Additionally, novel computational methods allow accurate estimation of transcript ...

The recently introduced Kallisto pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments.  Researchers from the Keck School of Medicine of USC offer cloud-scale RNAseq pipelines Arkas-Quantification, which deploys Kallisto for parallel cloud computations, and Arkas-Analysis, which annotates ...

Novel single-cell transcriptome sequencing assays allow researchers to measure gene expression levels at the resolution of single cells and offer the unprecendented opportunity to investigate at the molecular level fundamental biological questions, such as stem cell differentiation or the discovery ...

Reproducible research is a key component of the scientific method and represents the ability of repeating an experiment in any place with any person. A study can be truly reproducible when it satisfies at least the following three criteria. – ...

Single cell RNA-seq is a powerful methodology. Nevertheless there are important limitations, including the technical challenges of breaking down an organ or tissue into a single cell suspension. Invariably this has required enzymatic incubation at 37°C, which can be expected ...

The single cell RNA sequencing (scRNA-seq) technique began a new era by allowing the observation of gene expression at the single cell level. However, there is also a large amount of technical and biological noise. Because of the low number ...

The amounts and types of available multimodal tumor data are rapidly increasing, and their integration is critical for fully understanding the underlying cancer biology and personalizing treatment. However, the development of methods for effectively integrating multimodal data in a principled ...

RNA sequencing (RNA-Seq) is a powerful technique for the gene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies. Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as ...

Measurement of gene expression levels for multiple genes in single cells provides a powerful approach to study heterogeneity of cell populations and cellular plasticity. While the expression levels of multiple genes in each cell are available in such data, the ...