Resources

Software & Resources

Protocols, computational tools, pipelines, and interactive resources developed by the Sai Ma Lab and collaborators.

ChromE-seq

ChromE-seq, a scalable single-cell assay that jointly profiles chromatin contacts and RNA in the same cells.

ME-seq

Step-by-step protocol for ME-seq.

Pipeline for processing ME-seq data from BCL or FASTQ files.

SHARE-seq

Step-by-step SHARE-seq protocol.

Updated pipeline for demultiplexing and aligning SHARE-seq ATAC and RNA data.

Original SHARE-seq alignment pipeline.

Computational Tools

Code associated with inferring regulatory relationships from paired chromatin-accessibility and gene-expression data.

Tool for identifying peak–gene associations from single-cell multi-omic data.

Interactive Data

Interactive exploration of lung tumor single-cell chromatin accessibility data.

Interactive exploration of regulatory networks from SHARE-seq skin data.

Interactive exploration of PBMC stimulation data associated with FigR.

Interactive exploration of fetal liver hematopoietic stem and progenitor cell data.

Genome-browser tracks for fetal liver chromatin accessibility data.