Circular RNAs (circRNAs) are involved in various biological processes and disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current...
Read More »Single-cell RNA and protein expression in relation to cell cycle progression
Today researchers within the Human Protein Atlas (HPA) publish a study of single-cell RNA and protein expression in relation to cell cycle progression in...
Read More »Single-cell mapper (scMappR) – using scRNA-seq to infer the cell-type specificities of differentially expressed genes
RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on...
Read More »TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
The use of RNA-Seq data and the generation of de novo transcriptome assemblies have been pivotal for studies in ecology and evolution. This is distinctly true for non-model organisms, where no genome information is available; yet, studies of differential gene ...
Read More »lncEvo – automated identification and conservation study of long noncoding RNAs
Long noncoding RNAs represent a large class of transcripts with two common features: they exceed an arbitrary length threshold of 200 nt and are...
Read More »The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
The RNA integrity number (RIN) is a frequently used quality metric to assess the completeness of rRNA, as a proxy for the corresponding mRNA in a tissue...
Read More »SpatialDWLS – accurate deconvolution of spatial transcriptomic dat
Recent development of spatial transcriptomic technologies has made it possible to systematically characterize cellular heterogeneity while preserving spatial information, which greatly enables the investigation of structural organization of a tissue and its impact on modulating cellular behavior. On the other ...
Read More »A multi-center cross-platform single-cell RNA sequencing reference dataset
Single-cell RNA sequencing (scRNA-seq) is developing rapidly, and investigators seeking to use this technology are left with a variety of options...
Read More »BatchBench – flexible comparison of batch correction methods for single-cell RNA-seq
As the cost of single-cell RNA-seq experiments has decreased, an increasing number of datasets are now available. Combining newly generated and publicly accessible datasets is challenging due to non-biological signals, commonly known as batch effects...
Read More »McSplicer – a probabilistic model for estimating splice site usage from RNA-seq data
Alternative splicing removes intronic sequences from transcripts in alternative ways to produce different forms (isoforms) of mature mRNA. The composition of expressed transcripts and their alternative forms give specific functionalities to cells in a particular...
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