Single-cell analysis in Python. Scales to >100M cells.
🧬 gget enables efficient querying of genomic reference databases
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Annotated data.
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
Single cell perturbation prediction
starfish: unified pipelines for image-based transcriptomics
Python package to perform enrichment analysis from omics data.
Differential expression analysis for single-cell RNA-seq data.
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Identification of differential RNA modifications from nanopore direct RNA sequencing
Analyze your RNA sequencing data without writing a single line of code
Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
A tool to identify, orient, trim and rescue full length cDNA reads
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
𝒫robabilistic modeling of RNA velocity ⬱
Unsupervised Deep Disentangled Representation of Single-Cell Omics
The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
MERlin is an extensible analysis pipeline applied to decoding MERFISH data
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