Pooled CRISPR screens coupled with single-cell RNA-sequencing have enabled systematic interrogation of gene function and regulatory networks. Researchers from the New York Genome Center have developed...
Read More »ParslRNA-Seq – an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression
RNA sequencing has become an increasingly affordable way to profile gene expression analyses. Researchers from the LNCC, Brazil have developed a scientific workflow implementing several open...
Read More »WASP – a versatile, web-accessible single cell RNA-Seq processing platform
The technology of single cell RNA sequencing (scRNA-seq) has gained massively in popularity as it allows unprecedented insights into cellular heterogeneity as well as identification and characterization of (sub-)cellular populations. Furthermore...
Read More »A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity
Individual cells can assume a variety of molecular and phenotypic states and recent studies indicate that cells can rapidly adapt in response to...
Read More »Bulk2Space – de novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution
Uncovering the tissue molecular architecture at single-cell resolution could help better understand organisms' biological and pathological processes. However, bulk RNA-seq can only measure gene expression in cell mixtures, without revealing the...
Read More »miRPipe – a unified computational framework for a robust, reliable, and reproducible identification of novel miRNAs from RNA sequencing data
In eukaryotic cells, miRNAs regulate a plethora of cellular functionalities ranging from cellular metabolisms, and development to the regulation of biological...
Read More »Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells
Sophisticated methods to properly pre-process and analyze the increasing collection of single-cell RNA sequencing (scRNA-seq) data are increasingly...
Read More »Entropy sorting of single-cell RNA sequencing data to discern meaningful cellular heterogeneity from technical or biological noise
A team led by researchers at the Wellcome-MRC Cambridge Stem Cell Institute has developed entropy sorting (ES), a mathematical framework that distinguishes genes indicative of cell identity...
Read More »CellMap – in silico cell type decomposition is an efficient, inexpensive, and convenient alternative to scRNA-Seq that can leverage bulk RNA-seq
Induced pluripotent stem cell (iPSC) derived cell types are increasingly employed as in vitro model systems for drug discovery. For these studies to be meaningful, it is important to understand the reproducibility of the iPSC-derived cultures and their...
Read More »Sparse group lasso outperforms other penalized regression methods for gene (feature) selection from scRNA-seq data
With the emergence of single-cell RNA sequencing (scRNA-seq) technology, scientists are able to examine gene expression at single-cell resolution. Analysis of scRNA-seq data has its own challenges...
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