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…
Browsing: Other Tools
STRIDE – a topic-model-based method to deconvolve spatial transcriptomics using scRNA-seq
The recent advances in spatial transcriptomics have brought unprecedented opportunities to understand the cellular heterogeneity…
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…
Circ-LocNet – a computational framework for circular RNA sub-cellular localization prediction
Circular ribonucleic acids (circRNAs) are novel non-coding RNAs that emanate from alternative splicing of precursor…
scTagger – a computational method to match cellular barcodes data from long-reads and short-reads
Single-cell RNA sequencing allows for characterizing the gene expression landscape at the cell type level.…
A comprehensive analytical protocol to interrogate multiple single-cell RNA-seq datasets with SingCellaR
Single-cell RNA sequencing has led to unprecedented levels of data complexity. Although several computational platforms…
viRNAtrap – a package to generate predicted viral contigs from unmapped RNA-seq reads
About 15% of human cancer cases are attributed to viral infections. To date, virus expression…
A deep learning model to classify neoplastic state and tissue origin from transcriptomic data
Application of deep learning methods to transcriptomic data has the potential to enhance the accuracy…
WAT3R – Recovery of T Cell Receptor Variable Regions From 3’ Single-Cell RNA-Sequencing
Diversity of the T cell receptor (TCR) repertoire is central to adaptive immunity. The TCR…
RNA-MuTect-WMN – Estimating tumor mutational burden from RNA-sequencing without a matched-normal sample
Detection of somatic mutations using patients sequencing data has many clinical applications, including the identification…