Massively parallel DNA sequencing has led to the rapid growth of highly multiplexed experiments in biology. These experiments produce unique sequencing results that require specific analysis...
Read More »CaRPool-seq – combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq
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 »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 »LAPA – analysis of alternative polyadenylation from long-read or short-read RNA-seq
Alternative polyadenylation (APA) is a major mechanism that increases transcriptional diversity and regulates mRNA abundance. Existing computational tools to analyze APA have low precision because these tools are designed for short-read RNA-seq, which is a suboptimal data source to study ...
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 »CAPITAL – alignment of single-cell trajectory trees
Global alignment of complex pseudotime trajectories between different single-cell RNA-seq datasets is challenging, as existing tools mainly focus on linear alignment of single-cell trajectories...
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 »scIMC – a platform for benchmarking comparison and visualization analysis of scRNA-seq data imputation methods
With the advent of single-cell RNA sequencing (scRNA-seq), one major challenging is the so-called ‘dropout’ events that distort gene expression and remarkably influence downstream analysis in single-cell...
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