GONetView

Aggregate results from bioinformatics analyses across many samples into a single report.

NOS-TLPlot is an open-source tool for visualizing Newcastle–Ottawa Scale (NOS) risk-of-bias assessments in systematic reviews. It converts NOS star ratings into publication-ready traffic-light plots and 12 specialized visualizations, enabling reviewers and readers to interpret study-level risk-of-bias results clearly and reproducibly.

pyLocusZoom is an open-source Python library for visualizing genome-wide association study (GWAS) results. It creates LocusZoom-style regional association plots with linkage disequilibrium (LD) coloring, gene and exon tracks, and recombination overlays. Additional plots include Manhattan, QQ, Miami, eQTL, fine-mapping credible sets, PheWAS, forest plots, LD heatmaps and colocalization comparisons. Matplotlib provides static figures; Plotly and Bokeh provide interactive views. The library accepts pandas DataFrames and includes loaders for PLINK, GEMMA, REGENIE, BOLT-LMM, SAIGE, GTEx, SuSiE and FINEMAP outputs. It supports canine and feline reference data, automatic Ensembl gene annotations, and custom reference data for other species. LD can be supplied or calculated with PLINK. Requires Python 3.10 or later and is released under GPL-3.0-or-later.

Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the [Open Bioinformatics Foundation](http://open-bio.org/). Contains the very useful [Entrez](https://biopython.org/DIST/docs/api/Bio.Entrez-module.html) package for API access to the NCBI databases.

Fast, interactive, multi-dimensional image viewer for Python, foundational platform for scientific imaging AI with a rich plugin ecosystem integrating deep learning segmentation, object tracking, and microscopy analysis workflows (2.6K+ stars)

Scalable toolkit for analyzing single-cell gene expression data, including preprocessing, visualization, clustering, and trajectory inference.