Single-cell chromatin state analysis with Signac | Nature Methods
The recent development of experimental methods for measuring chromatin state at single-cell resolution has created a need for computational tools capable of analyzing these datasets. Here researchers developed Signac, a comprehensive toolkit for the analysis of single-cell chromatin data. Signac enables an end-to-end analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis and interactive visualization.
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders | Nature Genetics
Irritable bowel syndrome (IBS) results from disordered brain–gut interactions. Identifying susceptibility genes could highlight the underlying pathophysiological mechanisms. Researchers designed a digestive health questionnaire for UK Biobank and combined identified cases with IBS with independent cohorts. They conducted a genome-wide association study with 53,400 cases and 433,201 controls and replicated significant associations in a 23andMe panel (205,252 cases and 1,384,055 controls). This study identified and confirmed six genetic susceptibility loci for IBS. Implicated genes included NCAM1, CADM2, PHF2/FAM120A, DOCK9, CKAP2/TPTE2P3 and BAG6. The first four are associated with mood and anxiety disorders, expressed in the nervous system, or both.
Run AlphaFold v2.0 on Amazon EC2 | AWS Machine Learning Blog
After the article in Nature about the open-source of AlphaFold v2.0 on GitHub by DeepMind, many in the scientific and research community have wanted to try out DeepMind’s AlphaFold implementation firsthand. In this post, the author provides you with step-by-step instructions on how to install AlphaFold on an EC2 instance with Nvidia GPU.