Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20 and 80% of eukaryoti...
Transposable Elements (TEs) contribute to the repetitive fraction in almost every eukaryotic genome known to date, and their transcriptional activation can influence the expression of neighboring genes in healthy and disease states. Single cell RNA-Seq (scRNA-Seq) is a technical advance that allows ...
If using the software in a publication, please cite thefollowing: Jin Y, Tam OH, Paniagua E, Hammell M. (2015) TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics. 31(22):3593-9....
Global changes in DNA methylation are observed in development and disease, and single-cell analyses are highlighting the heterogeneous regulation of these processes. However, technical challenges associated with single-cell analysis of DNA methylation li
In order to identify the genes that change their expression in pulmonary cell lines (Calu-3, MRC-5, A549, and NHBE) due to infection of Coronaviruses such as MERS-CoV, SARS-CoV, or SARS-CoV-2, differential expression analysis was performed in RNA-seq data (Supplementary Table 1). As ...