python module to plot beautiful and highly customizable genome browser tracks

ENCODE ChIP-seq pipeline

The web interface for U-FISH

抓取网络文章到github issues保存

An introduction to various methods/approaches for the analysis of peaks generated from ChIP-seq / CUT&RUN / ATAC-seq

NicheNet: predict active ligand-target links between interacting cells

R toolkit for inference and analysis of pathway-mediated cell-cell communication chain from single-cell transcriptomics

Deep learning based spot detection for FISH images.

Data toolkits for processing NMR, MALDI MSI, MALDI single cell, Raman Spectroscopy, LC-MS and GC-MS raw data, chemoinformatics data analysis and data visualization.

ENCODE ATAC-seq pipeline

R package to access DoRothEA's regulons

Custom Jupyter Notebook Themes

为GPT/GLM等LLM大语言模型提供实用化交互接口，特别优化论文阅读/润色/写作体验，模块化设计，支持自定义快捷按钮&函数插件，支持Python和C++等项目剖析&自译解功能，PDF/LaTex论文翻译&总结功能，支持并行问询多种LLM模型，支持chatglm3等本地模型。接入通义千问, deepseekcoder, 讯飞星火, 文心一言, llama2, rwkv, claude2, m…

starfish: unified pipelines for image-based transcriptomics

Spatial alignment of single cell transcriptomic data.

Application for making ENCODE Blacklists

Louvain Community Detection

Detecting sites of genomic enrichment

MACS -- Model-based Analysis of ChIP-Seq

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard