A framework to score and analyze variant effects genome-wide using ChromBPNet models

A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.

Single-cell ATAC-seq analysis via Latent feature Extraction

scOpen: single-cell open chromatin analysis via NMF modelling

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

ggplot everything

IPython magic command to format python code in cell using black.

ggideogram is a ggplot2 extension package for drawing chromosome diagrams

A single-cell multimodal omics method for simultaneously detecting chromatin architecture and mRNA expression by sequencing (scCARE-seq)

Simple examples of common data and organization types used to vizualize data in the UCSC Genome Browser using Track Hubs

💔 An implementation of scale functions for setting axis breaks of a 'gg' plot.

VS Code in the browser

supporting scripts for manuscript Liu, Morgan et al. (2014) High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline. Genetics. doi:10.153…

Importing and manipulating Hi-C data in R

Peak caller for CUT&TAG data

SEACR: Sparse Enrichment Analysis for CUT&RUN

Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

chia pet analysis software

Simple utility to concatenate .fastq(.gz) files whilst creating a summary of the sequences.

Statistically Significant loops from HiChIP data

Free ChatGPT&DeepSeek API Key，免费ChatGPT&DeepSeek API。免费接入DeepSeek API和GPT4 API，支持 gpt | deepseek | claude | gemini | grok 等排名靠前的常用大模型。

ROSE: RANK ORDERING OF SUPER-ENHANCERS

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment