Software

3D Genomics & Epigenomics

Software tools developed and maintained by Minji & friends for analyzing 3D genome mapping data including (but not limited to) Hi-C, Micro-C, ChIA-PET, PLAC-seq, HiChIP, ChIA-Drop, SPRITE, Pore-C. Also includes tools for analyzing 1-dimensional genomic assays such as ChIP-seq, CUT&Tag, CUT&RUN, and ATAC-seq.

ChIA-Rep

• Description:

• GitHub:

• Publications: N/A. Please refer to its successor HiChIA-Rep.

• Main Developer: 

Chrom-Sig

• Description:

• GitHub:

• Publications: 

• Main Developer: 

HiChIA-Rep

• Description:

• GitHub:

• Reference: 

• Main Developer: 

MIA-Jet

• Purpose:

• GitHub:

• Publications: 

• Main Developer: 

MIA-Sig

• Purpose:

• GitHub:

• Publications: 

• Main Developer: 

pyBedGraph

• Purpose:

• GitHub:

• Publications: 

• Main Developer: 

Others Tools

Minji's early work on gene prioritization, genomic data compression, and genomic education. Also includes her collaborative projects ChIA-PIPE and ChIPWig.

HyDRA

• Description:

• GitHub:

• Reference: 

• Main Developer: 

MetaCRAM

• Purpose:

• GitHub:

• Publications: 

• Main Developer: 

TeachEnG

• Purpose:

• GitHub:

• Publications: 

• Main Developer: