Software Updates

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

Snakemake

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.

PyMOL Open Source

open source version of the widely used molecular visualization package developed by Warren DeLano.

pySCENIC

is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

scDRS

(single-cell disease-relevance score) is a method for associating individual cells in scRNA-seq data with disease GWASs, built on top of AnnData and Scanpy.

R

a free software environment for statistical computing and graphics.