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Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seamless integration with rhdf5, however the compiled filters can also be used with external applications.

Evolvable and privacy-preserving multi-agent framework automating, scaling, and accelerating data sciences with a particular focus on end-to-end single-cell biology analyses; features agentic code evolution, multi-agent team orchestration, distributed architecture, and a community marketplace with 1,000+ curated agents and skills (428+ stars)

JCVI is a versatile toolkit for comparative genomics analysis. It is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

Databank of optimised macromolecular structures. PDB-REDO entries are refined, rebuilt and validated with one consistent protocol using the equivalent entry in the Protein Data Bank and its experimental data. PDB-REDO entries typically have higher structural quality and a better fit to the experimental data.

A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)

Unified ML/DL framework for drug discovery workflows, integrating RDKit, DeepChem, and scikit-learn with SHAP explainability

The kallisto | bustools pipeline is a fast and modular set of tools to convert single cell RNA-seq reads in fastq files into gene count or transcript compatibility counts (TCC) matrices for downstream analysis. Central to this pipeline is the barcode, UMI, and set (BUS) file format. This package serves the following purposes: First, this package allows users to manipulate BUS format files as data frames in R and then convert them into gene count or TCC matrices. Furthermore, since R and Rcpp code is easier to handle than pure C++ code, users are encouraged to tweak the source code of this package to experiment with new uses of BUS format and different ways to convert the BUS file into gene count matrix. Second, this package can conveniently generate files required to generate gene count matrices for spliced and unspliced transcripts for RNA velocity. Here biotypes can be filtered and scaffolds and haplotypes can be removed, and the filtered transcriptome can be extracted and written to disk. Third, this package implements utility functions to get transcripts and associated genes required to convert BUS files to gene count matrices, to write the transcript to gene information in the format required by bustools, and to read output of bustools into R as sparses matrices.

Create an index on a compressed text file.

Embeddable genome viewer. Integration data from a wide variety of sources, and can load data directly from popular genomics file formats including bigWig, BAM, and VCF.

Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays.