Analysis Pipelines

Single-cell/nuclei RNA-sequencing (scRNA-seq) technologies can simultaneously quantify gene expression in thousands of cells across the genome. However, the majority of the noncoding RNAs, such as microRNAs (miRNAs), cannot currently be profiled at the same scale. MiRNAs are a class of ...

Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have been used to measure transcription levels in biological...

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...

Genomic profiling using short-read sequencing has utility in detecting disease-associated variation in both DNA and RNA. However, given the frequent occurrence of structural variation in cancer, molecular...

Single-cell technologies have revolutionised biological research and applications. As they continue to evolve with multi-omics and spatial resolution, analysing single-cell datasets is becoming...

The recent advance of single cell sequencing (scRNA-seq) technology such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) allows researchers to quantify cell surface protein...

Cellenics® is an open-source software that enables researchers to perform single-cell RNA sequencing (scRNA-seq) data analysis without writing a single line of code.  Cellenics® software was developed by © 2020-2022 President and Fellows of Harvard College. Biomage is an open-source ...

Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq...

Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial..

Genetic and epigenetic biological studies often combine different types of experiments and multiple conditions. While the corresponding raw and processed data are made available through specialized public databases, the processed files are usually limited to a specific research question. Hence, ...