transcriptomics

Single-cell analysis in Python. Scales to >1M cells.

An interactive explorer for single-cell transcriptomics data

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.

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

starfish: unified pipelines for image-based transcriptomics

Fusing Histology and Genomics via Deep Learning - IEEE TMI

Single cell perturbation prediction

R package for analyzing single-cell RNA-seq data

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Differential expression analysis for single-cell RNA-seq data.

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

Brings bulk and pseudobulk transcriptomics to the tidyverse

A list of web-based interactive biological data visualizations.

Identification of differential RNA modifications from nanopore direct RNA sequencing

An ontology of cell types

Reference-guided transcript discovery and quantification for long read RNA-Seq data

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data