Resources
Software & Resources
Protocols, computational tools, pipelines, and interactive resources developed by the Sai Ma Lab and collaborators.
ME-seq step-by-step protocol
Step-by-step protocol for ME-seq.
ME-seq alignment pipeline
Pipeline for processing ME-seq data from BCL or FASTQ files.
SHARE-seq V1 step-by-step protocol
Step-by-step SHARE-seq protocol.
SHARE-seq alignment pipeline v2.0
Updated pipeline for demultiplexing and aligning SHARE-seq ATAC and RNA data.
SHARE-seq alignment pipeline v1.0
Original SHARE-seq alignment pipeline.
Functional Inference of Gene Regulation (FigR)
Code associated with inferring regulatory relationships from paired chromatin-accessibility and gene-expression data.
fastDORC
Tool for identifying peak–gene associations from single-cell multi-omic data.
scATAC lung tumor atlas
Interactive exploration of lung tumor single-cell chromatin accessibility data.
SHARE-seq skin network
Interactive exploration of regulatory networks from SHARE-seq skin data.
PBMC stimulation data exploration
Interactive exploration of PBMC stimulation data associated with FigR.