RNA-seq aligner
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Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Fast, sensitive and accurate integration of single-cell data with Harmony
Spatial Single Cell Analysis in Python
- single-cell-rna-seq
- single-cell-genomics
- spatial-transcriptomics
- spatial-analysis
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.
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.
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
scPerturb: A resource and a python/R tool for single-cell perturbation data
- cite-seq
- database
- perturbation
- scatac-seq
🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
Autonomous multi-agent framework to optimize scientific software
- acceleration
- agentic-ai
- ai-agents
- bioinformatics
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
- single-cell
- scrna-seq
- scatac-seq
- deep-neural-networks