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…
Browsing: Analysis Pipelines
Cogito – automated and generic comparison of annotated genomic intervals
Genetic and epigenetic biological studies often combine different types of experiments and multiple conditions. While…
Pinc – a bioinformatic-assisted workflow for genome-wide identification of ncRNAs
With the upcoming of affordable Next-Generation Sequencing technologies, the number of known non-protein coding RNAs…
scGENA – a single-cell gene coexpression network analysis framework for clustering cell types and revealing biological mechanisms
Single-cell RNA-sequencing (scRNA-seq) is a recent high-throughput technique that can measure gene expression, reveal cell…
scraps – an end-to-end pipeline for measuring alternative polyadenylation at high resolution using single-cell RNA-seq
Alternative cleavage and polyadenylation (APA) contributes to the diversity of mRNA 3′ ends, affecting post-transcriptional…
aTAP – automated transcriptome analysis platform for processing RNA-seq data by de novo assembly
RNA-seq is a sequencing technique that uses next-generation sequencing (NGS) to explore and study the…
Kodoja – a workflow for virus detection in plants using k-mer analysis of RNA-sequencing data
RNA-sequencing of plant material allows for hypothesis-free detection of multiple viruses simultaneously. This methodology relies…
THRONE – a new approach for accurate prediction of human RNA N7-methylguanosine sites
N7-methylguanosine (m7G) is an essential, ubiquitous, and positively charged modification at the 5′ cap of…
Kassandra – precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes
Cellular deconvolution algorithms virtually reconstruct tissue composition by analyzing the gene expression of complex tissues.…
SMaSH – a scalable, general marker gene identification framework for single-cell RNA-sequencing
Single-cell RNA-sequencing is revolutionising the study of cellular and tissue-wide heterogeneity in a large number…