Single-cell RNA sequencing has led to unprecedented levels of data complexity. Although several computational platforms are available, performing data analyses for multiple datasets remains a significant challenge. University of Oxford researchers provide a comprehensive analytical protocol to interrogate multiple datasets ...
Read More »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 in tumor tissues has been mostly studied by aligning tumor...
Read More »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. Targeted single-cell mRNA-sequencing reduces sequencing costs by profiling reduced gene sets that capture biological information with a minimal number of genes. Caltech researchers have developed ...
Read More »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 workflow, called RNA-Seq-Pop, which...
Read More »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 is composed of α and β chains, encoded by the TRA and TRB...
Read More »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 the single-cell level and to inform...
Read More »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 of cancer driver genes, detection of mutational signatures, and estimation of...
Read More »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 and underpins much of what is known...
Read More »nf-rnaSeqCount – a Nextflow pipeline for obtaining raw read counts from RNA-seq data
The rate of raw sequence production through Next-Generation Sequencing (NGS) has been growing exponentially due to improved technology and reduced costs. This has enabled researchers to answer many biological questions through "multi-omics"...
Read More »FIRM – Flexible integration of single-cell RNA-sequencing data for large-scale multi-tissue cell atlas datasets
Single-cell RNA-sequencing (scRNA-seq) is being used extensively to measure the mRNA expression of individual cells from deconstructed tissues, organs and even entire organisms to generate cell atlas...
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