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abc-enhancer-gene-prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

anchor

This is the package of Yuanfang's winning algorithm in the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge

atac-seq

Basic workflow for ATAC-seq analysis

atac-seq-pipeline

ENCODE ATAC-seq pipeline

bard-google-extension-mini

Chat with Bard along side google search

bash-boilerplate

A collection of Bash scripts for creating safe and useful command line programs.

basic-browser

bedtoolsr

R package wrapping bedtools

blacklist

Application for making ENCODE Blacklists

c_practice

chia-pipe

ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization

chip-seq-pipeline

ENCODE Uniform processing pipeline for ChIP-seq

chipseeker

:dart: ChIP peak Annotation, Comparison and Visualization

chromhmm_mesc_mm10

Chromatin States Map in mouse embryonic stem cell

containers

Bioinformatics containers

cresil

CReSIL: Accurate Identification of Extrachromosomal Circular DNA from Long-read Sequences

deepbind

Training and testing of DeepBind models.

deepbind-with-pytorch

CNN architecture for predicting DNA binding sites for Transcription Factors

deeptools

Tools to process and analyze deep sequencing data.

dreamberd---e-acc

perfect programming language

ecc_pipe

enrichshuf

genomicdistributions

Calculate and plot distributions of genomic ranges

giggle

Interval data structure

hello-algo

《Hello 算法》：动画图解、一键运行的数据结构与算法教程，支持 Java, C++, Python, Go, JS, TS, C#, Swift, Rust, Dart, Zig 等语言。

hotspot

Hotspot is a program for identifying genomic regions of local enrichment of short-read sequence tags.

infranodus

jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser

jeme

JEME method for predicting enhancer targets

multiz

DNA multiple sequence aligner, official version from Penn State's Miller Lab