The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome-millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of traditional ap...
Large compendia of gene expression data have proven valuable for the discovery of novel biological relationships. Historically, most available RNA assays were run on microarray, while RNA-seq is now the platform of choice for many new experiments. Th...
Single-cell RNA sequencing (scRNA-seq) data scale surges with high-throughput sequencing technology development. However, although single-cell data analysis is a powerful tool, various issues have been reported, such as sequencing sparsity and comple...
Cross-species comparative analyses of single-cell RNA sequencing (scRNA-seq) data allow us to explore, at single-cell resolution, the origins of the cellular diversity and evolutionary mechanisms that shape cellular form and function. Cell-type assig...
Genomics, proteomics & bioinformatics
Dec 14, 2022
Single-cell RNA sequencing (scRNA-seq) has become a routinely used technique to quantify the gene expression profile of thousands of single cells simultaneously. Analysis of scRNA-seq data plays an important role in the study of cell states and pheno...
Spatially resolved scRNA-seq (sp-scRNA-seq) technologies provide the potential to comprehensively profile gene expression patterns in tissue context. However, the development of computational methods lags behind the advances in these technologies, wh...
We describe a protocol to perform fast and non-arbitrary quality control of single-cell RNA sequencing (scRNA-seq) raw data using scKB and COPILOT. scKB is a wrapper script of kallisto and bustools for accelerated alignment and transcript count matri...
With the advent of single cell/nucleus RNA sequencing (sc/snRNA-seq), the field of cell phenotyping is now a data-driven exercise providing statistical evidence to support cell type/state categorization. However, the task of classifying cells into sp...
RNA-binding proteins (RBPs) are key co- and post-transcriptional regulators of gene expression, playing a crucial role in many biological processes. Experimental methods like CLIP-seq have enabled the identification of transcriptome-wide RNA-protein ...
Environmental pollution (Barking, Essex : 1987)
Dec 4, 2019
Cypermethrin is a frequently used insecticide in agriculture and households but its chronic and molecular effects are poorly known are . Here we describe effects of sublethal cypermethrin exposure on the global transcriptome in the brain of honey bee...