miRPipe – identification of novel miRNAs from RNA sequencing data
In eukaryotic cells, miRNAs regulate a plethora of cellular functionalities ranging from cellular metabolisms, and…
Browsing: Analysis Pipelines
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…
ActiveSVM – single-cell mRNA-seq data analysis with a minimal number of genes
Sequencing costs currently prohibit the application of single-cell mRNA-seq to many biological and clinical analyses.…
RNA-Seq-Pop – Exploiting the sequence in RNA-Seq – a Snakemake workflow
Researchers at the Liverpool School of Tropical Medicine have developed a reproducible and scalable Snakemake…
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…
scAmpi – A versatile pipeline for single-cell RNA-seq analysis from basics to clinics
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique to decipher tissue composition at…
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…
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…