pathlinkR – analyze and interpret RNA-Seq results
RNA sequencing (RNA-Seq) is a powerful technique that helps researchers study gene expression, giving them…
Browsing: Pathway Analysis
DeepGSEA – explainable deep gene set enrichment analysis for single-cell transcriptomic data
Gene set enrichment (GSE) analysis is a crucial tool for interpreting gene expression data. It…
RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations
Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks…
Scan – scanning sample-specific miRNA regulation
RNA-sequencing technology provides an effective tool for understanding miRNA regulation in complex human diseases, including…
Pathway Analysis with OmicsBox: Analyzing a Salamander Limb Regeneration Transcriptomics Dataset
The functional interpretation of differentially expressed genes obtained from RNA-seq data is a critical step…
Single-cell gene set enrichment analysis and transfer learning for functional annotation of scRNA-seq data
Although an essential step, cell functional annotation often proves particularly challenging from single-cell transcriptional data.…
IReNA – Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles
Recently, single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) have…
BoT-Net – a lightweight bag of tricks-based neural network for efficient LncRNA–miRNA interaction prediction
Interactions of long non-coding ribonucleic acids (lncRNAs) with micro-ribonucleic acids (miRNAs) play an essential role…
CLIPreg – Constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq
The creation and analysis of gene regulatory networks have been the focus of bioinformatics research…
SPIRAL – Significant Process InfeRence ALgorithm for single cell RNA-sequencing and spatial transcriptomics
Gene expression data is complex and may hold information regarding multiple biological processes at once.…