Membrane Visual QC

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.

Pythonic access to FASTA files.

Large-scale benchmark suite for protein fitness prediction and design, aggregating 200+ deep mutational scanning assays and clinical variant datasets across diverse protein families and taxa, with standardized zero-shot and supervised leaderboards for variant effect prediction, mutation effect prediction, and protein language model evaluation (OATML & Marks Lab, NeurIPS 2023 Spotlight, Datasets & Benchmarks)

A swiss army knife for manipulating and editing PDB files.

SQUARNA is a tool for RNA secondary structure prediction. It can take a single RNA sequence or an alignment of sequences as input. SQUARNA handles pseudoknots and can predict alternative structures. SQUARNA allows structural restraints and chemical probing data as additional input and is available at https://github.com/febos/SQUARNA and https://larnal.imol.institute/.

HIDE-Deconv is a framework for characterizing cellular remodeling from bulk RNA-seq data using hierarchical cell-type deconvolution across multiple levels of cellular resolution. It provides an integrated workflow for single-cell reference preprocessing, estimation of cellular compositions, and downstream analysis of deconvolution results, including visualization, clustering, differential composition, and survival analysis.