Repository Index

Official git repository for Biopython (originally converted from CVS)

• python
• bioinformatics
• genomics
• biopython

RNA-seq aligner

Deep probabilistic analysis of single-cell and spatial omics data

• scrna-seq
• variational-bayes
• variational-autoencoder
• cite-seq

🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.

• ai-agents
• bioinformatics
• equity
• genomics

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

C library for high-throughput sequencing data formats

• htslib
• bioinformatics
• sam
• bam

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

• dna
• k-mer
• python
• bloom-filter

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

• kmer
• dnabert-model
• kmer-format
• gpu

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

• deep-learning
• protein-sequences
• protein-structure
• semi-supervised-learning

A Go package for engineering organisms.

• synthetic-biology
• synbio
• genetic-engineering
• molecular-biology

Generation of protein sequences and evolutionary alignments via discrete diffusion models

• discrete-diffusion
• generative-model
• multiple-sequence-alignment
• protein-sequences

Fast, sensitive and accurate integration of single-cell data with Harmony

• scrna-seq
• algorithm
• data-integration
• r

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

• sequence-alignment
• edit-distance
• levehnstein-distance
• library

Spatial Single Cell Analysis in Python

• single-cell-rna-seq
• single-cell-genomics
• spatial-transcriptomics
• spatial-analysis

R package for detecting doublets in single-cell RNA sequencing data

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

Sequential regulatory activity predictions with deep convolutional neural networks.

Reference mapping for single-cell genomics

• single-cell
• deep-learning
• rna-seq-analysis
• data-integration

Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk

• bioinformatics
• exact-optimization
• metabolomics
• paired-data

RNA-seq prediction with deep convolutional neural networks.

Bi-Directional Equivariant Long-Range DNA Sequence Modeling

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

• cancer-genomics
• cnv-detection
• single-cell
• phylogeny

Genomic sequence storage, indexing and alignment inside PostgreSQL: https://bioseqdb.com/

• alignment
• bioinformatics
• biology
• database