UPDATED: April 16, 2024 nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow. This post will walk you through running the nf-core RNA-Seq workflow. The pipeline uses the STAR aligner by default, and quantifies data using Salmon, providing gene/transcript counts and extensive quality Read more…
In the Kenneth Birnbaum Lab, we are interested in understanding how the plant root is able to grow continuously over the plant’s life and maintain its specific root structure (Fig.1). More specifically, what is the role of the stem cells present at the very tip of the root (QC and Read more…
The bioinformatics team at the NYU Center for Genomics and Systems Biology in Abu Dhabi and New York have recently developed NASQAR (Nucleic Acid SeQuence Analysis Resource), a web-based platform providing an intuitive interface to popular R-based bioinformatics data analysis and visualization tools including Seurat, DESeq2, Shaman, clusterProfiler, and more. Read more…
Salmon and kallisto might sound like a tasty entree from a hip Tribeca restaurant, but the duo are in fact a pair of next-generation applications for rapid transcript quantification. They represent a new approach to transcript quantification using NGS that has a number of advantages over existing alignment-based methods. I’ve Read more…