PERFUMES – pipeline to extract RNA FUnctional motifs and exposed structures
Up to 75% of the human genome encodes RNAs. The function of many non-coding RNAs…
Browsing: Analysis Pipelines
scDisInFact – disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data
Single-cell RNA-sequencing (scRNA-seq) has been widely used for disease studies, where sample batches are collected…
betAS – intuitive analysis and visualisation of differential alternative splicing using beta distributions
Next generation RNA sequencing allows alternative splicing (AS) quantification with unprecedented resolution, with the relative…
NanOlympicsMod – benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing
N6-methyladenosine (m6A) is the most abundant internal eukaryotic mRNA modification, and is involved in the…
CAP-RNAseq – an integrated pipeline for functional annotation and prioritization of co-expression clusters
Cluster analysis is one of the most widely used exploratory methods for visualization and grouping…
SURGE – uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models
Genetic regulation of gene expression is a complex process, with genetic effects known to vary…
scFed – federated learning for cell type classification with scRNA-seq
The advent of single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity and…
Cellograph – a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks
With the growing number of single-cell datasets collected under more complex experimental conditions, there is…
STIGMA – Single-cell tissue-specific gene prioritization using machine learning
Clinical exome and genome sequencing have revolutionized the understanding of human disease genetics. Yet many…
scSNV-seq – high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics
CRISPR screens with single-cell transcriptomic readouts are a valuable tool to understand the effect of…