This repository will serve as a well of information, all regarding the analysis of bulk- and single-cell RNA-Seq experiments. I will try to include here tools I would like to test, sources of information regarding analysis and everything I can think of related to RNA-Seq.
Zero-inflated Negative Binomial based Wanted Variation Extraction (ZINB-WaVE)
ZINB-WaV leads to low-dimensional representations of the data that account for zero inflation (dropouts), over-dispersion, and the count nature of the data. We demonstrate, with simulated and real data, that the model and its associated estimation procedure are able to give a more stable and accurate low-dimensional representation of the data than principal component analysis (PCA) and zero-inflated factor analysis (ZIFA), without the need for a preliminary normalization step.
This repo contains the ClustAssess R package, which provides a set of tools for evaluating clustering robustness.