Single-Cell Analysis in Python. Scales to >1M cells.

An interactive explorer for single-cell transcriptomics data

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

R package for analyzing single-cell RNA-seq data

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

starfish: unified pipelines for image-based transcriptomics

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

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

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

just annotate it, dammit!

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

Brings transcriptomics to the tidyverse

Multi-sample Unified Discriminant ANalysis

Hierarchical, iterative clustering for analysis of transcriptomics data in R

A tool to identify, orient, trim and rescue full length cDNA reads

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

Fusing Histology and Genomics via Deep Learning.

Tools to annotate genomes using long read transcriptomics data

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature

Pipeline for annotating genomes using long read transcriptomics data with pinfish

(formerly eelpond) an automated RNA-Seq workflow system

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Detection of differential RNA modifications from direct RNA sequencing

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

Expression Weighted Celltype Enrichment