Paper Summary: Systematic bias and batch effects in single-cell RNA-Seq data




Single Cell RNA-seq technology has gained a lot of traction in the last few years, as it can help address a variety of interesting biological problems, ranging from studying development to cancer heterogeneity.  Since the first paper demonstrating the feasibility of single cell transcriptomics with, the number of cells one could assay is also increasing […]

Paper Summary: Fast and accurate single-cell RNA-seq analysis using equivalence class counts




One of the most common applications of single-cell RNA-seq data is to use it to characterize the heterogeneity of  cell populations and identify new cell types or sub-populations.  Typically one uses single-cell RNA-sequencing (RNA-seq) data, quantify gene expression on all cells and use the common gene-expression profile among the cells to characterize the cell-to-cell heterogeneity by […]

Inferring Cellular Localization from Single Cell RNA-seq




Thanks to RNA-seq, we have ways to estimate expression abundances decently (at least at gene level :-)).  One of the other missing dimensions in realm of  expression is where is that transcript expressed from? what is the physical location of the transcript?. Till recently, our ability to answer the positional information about the expressing transcript […]

Two Single-Cell RNA-seq Papers This Week




Just when you thought you finished reading an interesting single-cell RNA-seq paper, two more interesting papers come out on the same week: one in Nature and the other in Nature. I am not even going to summarize the papers now, other than saying that the Nature paper looks at single-cell RNA-seq data from over 1700 […]

Bayesian Approach to Single-Cell RNA-Seq Differential Expression Analysis




Just a few weeks ago Nature Methods published an interesting paper on Bayesian approach that takes care of technical variations in Single Cell RNA-seq data and perform differential expression analysis . This is one of many interesting papers that came out recently addressing technical variations in single-cell RNA-seq data. Bayesian approach to single-cell differential expression […]