This project is work in progress! https://www.sc-best-practices.org

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

Repository to host tool-specific module files for the Nextflow DSL2 community!

A rust framework to make using alevin-fry even simpler

User information about ScPCA processing

Multi-omics factor analysis v2

This is the alpha version of the CellOracle package

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

GenomicRanges in Python

Create QC and summary reports for Alevin output

Differential transcript and gene expression, as well as helper functions for working with Salmon, alevin, and alevin-fry data.

Clone of the Bioconductor repository for the DropletUtils package.

Useful scripts and tools related to alevin-fry

Significance analysis for clustering single-cell RNA-sequencing data

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

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

RNA Velocity generalized through dynamical modeling