RNA-seq aligner
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Deep probabilistic analysis of single-cell and spatial omics data
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
A tool for semi-automatic cell type classification
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
Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk
RNA-seq prediction with deep convolutional neural networks.
Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
Genomic sequence storage, indexing and alignment inside PostgreSQL: https://bioseqdb.com/
scPerturb: A resource and a python/R tool for single-cell perturbation data
🏃 The go-to single-cell Foundation Model
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
Autonomous multi-agent framework to optimize scientific software
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.