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Web application and service for visualizing small- to medium-scale models of gene regulatory networks. It automatically lays out either an unweighted or weighted network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges and has general applicability.

From https://anndata.readthedocs.io/en/latest/ "Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray."

CalibraCurve is a computational tool designed to generate calibration curves for targeted mass spectrometry-based quantitative data. It is applicable to various omics disciplines, including proteomics, lipidomics, and metabolomics. The package also offers functionalities for data and calibration curve visualization and concentration prediction from new datasets based on the established curves.

Trackastra is a transformer-based cell-tracking tool for live-cell microscopy. It links already segmented cell instances across time by predicting associations between detections. It supports greedy tracking with or without cell divisions, optional ILP-based linking, pretrained tracking models, and export of tracked masks and lineage information in Cell Tracking Challenge format.

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data

Comprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX.