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: Analysis Pipelines
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…
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…
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…
Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures
The current lack of benchmark datasets with inbuilt ground-truth makes it challenging to compare the…
miRPipe – identification of novel miRNAs from RNA sequencing data
In eukaryotic cells, miRNAs regulate a plethora of cellular functionalities ranging from cellular metabolisms, and…
scISR – a novel method for single-cell data imputation using subspace regression
Recent advances in biochemistry and single-cell RNA sequencing (scRNA-seq) have allowed us to monitor the…
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…