Software Updates

MMseqs2

an ultra fast and sensitive sequence search and clustering suite

Cellpose

Cellpose-SAM: cell and nucleus segmentation with superhuman generalization. It can be optimized for your own data, applied in 3D, works on images with shot noise, (an)isotropic blur, undersampling, contrast inversions, regardless of channel order and object sizes.

scanpy

a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

ColabFold

an easy-to-use Notebook based environment for fast and convenient protein structure predictions.

R

a free software environment for statistical computing and graphics.

BLAST+

a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.

PyTorch

an open source deep learning platform that provides a seamless path from research prototyping to production deployment.

R

a free software environment for statistical computing and graphics.

PyTorch

an open source deep learning platform that provides a seamless path from research prototyping to production deployment.

nextclade

SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks

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.