Single-cell/nuclei pipeline for data derived from Oxford Nanopore

This Workflow takes a dataset collection of single-cell ATAC-seq fragments and performs:

• preprocessing
• filtering
• concatenation
• dimension reduction
• batch correction (with Harmony and optionally Scanorama and MNC-correct)
• leiden clustering

• new SnapATAC2 version: from 2.5.3 to 2.6.4

Spatial Transcriptomics

Pipeline for processing 10x Genomics single cell rnaseq data

Pipeline for analysis of Molecular Pixelation assays

An analysis pipeline for Molecular Cartography data from Resolve Biosciences.

MARS-seq v2 preprocessing pipeline