Cogito – automated and generic comparison of annotated genomic intervals
Genetic and epigenetic biological studies often combine different types of experiments and multiple conditions. While…
Browsing: Analysis Pipelines
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…
Gruffi – an algorithm for improved delineation of developmental trajectories in organoids and resemblance to in vivo data.
Organoids enable in vitro modeling of complex developmental processes and disease pathologies. Like most 3D cultures, organoids…