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MultiSpace(Single-cell Multi-omic Analysis In Space) is a computational framework that combines single-cell multi-omic data such as scCOOL-seq with spatial transcriptomic information.

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

[DEPRECATED, see https://immunarch.com/] tcR: an R package for immune receptor repertoire advanced data analysis.

Chromosome-length haplotype determination from Hi-C and external reference panels

A single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations

Circular binary segmentation algorithm for copy number data

Causal Inference for the Brave and True. A light-hearted yet rigorous approach to learning about impact estimation and causality.

DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data

Parse BAM and BAM index files in javascript for node and the browser

SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.

[REPLACED by https://github.com/antigenomics/mirpy] Post-analysis of immune repertoire sequencing data

Efficient genotyping bi-allelic SNPs on single cells

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

Clustering scRNAseq by genotypes

Notes on single-cell Hi-C technologies, tools, and data

Analysis corresponding to the paper "Dynamics of Chromatin Accessibility in Cortical Interneurons"

Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020

Dataset distribution for Seurat

Repository for mtscATAC-seq protocol paper

code associated with crane-nature-2015, 10.1038/nature14450

Bioinformatics analysis code.

R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.

Evaluate scHi-C imputation methods