Single-cell analysis in Python. Scales to >1M cells.
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Updated
May 10, 2024 - Python
Single-cell analysis in Python. Scales to >1M cells.
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
Differential expression analysis for single-cell RNA-seq data.
Python package to perform enrichment analysis from omics data.
Identification of differential RNA modifications from nanopore direct RNA sequencing
RNA sequencing analysis software
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
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 ⬱
Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
MERlin is an extensible analysis pipeline applied to decoding MERFISH data
🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data
The Zavolab Automated RNA-seq Pipeline
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