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…
Browsing: Other Tools
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…
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…
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…
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…