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…
Browsing: Analysis Pipelines
Sparse group lasso outperforms other penalized regression methods for gene (feature) selection from scRNA-seq data
With the emergence of single-cell RNA sequencing (scRNA-seq) technology, scientists are able to examine gene…
PPMS – A framework to Profile Primary MicroRNAs from Single-cell RNA-sequencing datasets
Single-cell/nuclei RNA-sequencing (scRNA-seq) technologies can simultaneously quantify gene expression in thousands of cells across the…
CoRMAP – comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets
Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array…
SoloTE – improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression
Transposable Elements (TEs) contribute to the repetitive fraction in almost every eukaryotic genome known to…
PB_FLIP – PacBio Fusion and Long Isoform Pipeline for cancer transcriptome–based resolution of isoform complexity
Genomic profiling using short-read sequencing has utility in detecting disease-associated variation in both DNA and…
ShIVA – A user-friendly and interactive interface giving biologists control over their single-cell RNA-seq data
Single-cell technologies have revolutionised biological research and applications. As they continue to evolve with multi-omics…
scAllele – A versatile tool for the detection and analysis of variants in scRNA-seq
Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels.…
iCOMIC – a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data
Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can…
Cogito – automated and generic comparison of annotated genomic intervals
Genetic and epigenetic biological studies often combine different types of experiments and multiple conditions. While…