Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
- openworm
- elegans
- biology
- simulation
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An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
- fastq
- qc
- preprocessing
- filtering
A versatile pairwise aligner for genomic and spliced nucleotide sequences
- bioinformatics
- sequence-alignment
- spliced-alignment
- genomics
MMseqs2: ultra fast and sensitive search and clustering suite
- bioinformatics
- sequence-clustering
- profile-search
- sequence-search
Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released
- artificial-intelligence
- deep-learning
- protein-folding
- attention-mechanism
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
- bioinformatics
- cross-platform
- fasta
- golang
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
- ai-agents
- bioinformatics
- equity
- genomics
An open-source application for biological image analysis
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Cloud-native genomic dataframes and batch computing
- genetics
- vcf
- genomics
- gwas
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
- foundation-models
- genomics
- language-models
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
- dna
- k-mer
- python
- bloom-filter
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
- bioinformatics
- taxonomy
- cross-platform
- lineage
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
The repository host gives no description.
Probabilistic cell segmentation for in situ spatial transcriptomics
PhyloNetworks: a julia package with utilities for phylogenetic networks
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
- cellprofiler-analyst
- cellprofiler
- image-analysis
- machine-learning
🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
Interpretable bilinear attention network with domain adaptation improves drug-target prediction.
Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python