scAN1.0 – a reproducible and standardized pipeline for processing 10X single cell RNAseq data
Single cell transcriptomics has recently seen a surge in popularity, leading to the need for…
Browsing: Analysis Pipelines
Scaling up single-cell RNA-seq data analysis with CellBridge workflow
Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression at the individual cell…
SQANTI-SIM – a simulator of controlled transcript novelty for lrRNA-seq benchmark
Long-read RNA sequencing has emerged as a powerful tool for transcript discovery, even in well-annotated…
DREEP – predicting drug response from single-cell expression profiles of tumours
Intra-tumour heterogeneity (ITH) presents a significant obstacle in formulating effective treatment strategies in clinical practice.…
dsRID – in silico identification of dsRNA regions using long-read RNA-seq data
Double-stranded RNAs (dsRNAs) are potent triggers of innate immune responses upon recognition by cytosolic dsRNA…
Unraveling the timeline of gene expression – a pseudotemporal trajectory analysis of single-cell RNA sequencing data
Single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed in recent years. The droplet-based single cell…
RiboSplitter – prediction of alternative pre-mRNA splicing outcomes
To understand the biological impact of alternative pre-mRNA splicing, it is vital to know which…
RiboGalaxy – A Galaxy-based web platform for ribosome profiling data processing – 2023 Update
Ribosome profiling (Ribo-Seq) captures a “snapshot” of ribosomes’ locations at the entire transcriptome of a…
scTensor detects many-to-many cell–cell interactions from single cell RNA-sequencing data
Complex biological systems are described as a multitude of cell-cell interactions (CCIs). Recent single-cell RNA-sequencing…
sciCSR – infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data
Class-switch recombination (CSR) is an integral part of B cell maturation. Researchers at the University…