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 disease-relevance score) is a method for associating individual cells in scRNA-seq data with disease GWASs, built on top of AnnData and Scanpy.

a set of analysis pipelines that perform identification of open chromatin regions, motif annotation, and differential accessibility analysis for Single Cell ATAC data.

The set of analysis pipelines in this suite perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells.

a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.

a free software environment for statistical computing and graphics.

a reactive workflow framework and programming DSL that ease writing computational pipelines with complex data.

It is designed around the idea that the Linux platform is the lingua franca of data science. Linux provides many simple but powerful command-line and scripting tools that, when chained together, facilitate complex data manipulations.

Nextflow extends this approach, adding the ability to define complex program interactions and a high-level parallel computational environment based on the dataflow programming model.

A Nextflow script is defined by composing many different processes. Each process can be written in any scripting language that can be executed by the Linux platform (BASH, Perl, Ruby, Python, etc), to which is added the ability to coordinate and synchronize the processes execution by simply specifying their inputs and outputs.