Workflows for germline short variant discovery with GATK4

Intro to ChIPseq using HPC

Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods

RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.

Code for creating cell-type-specific regulatory element annotation files

Analysis package for processing counts from genome-wide CRISPR/Cas9 screens

Auto-analysis for Real-Time PCR (qPCR) data

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

📚 Freely available programming books

All-in-one analysis pipeline

List of libraries, tools and APIs for web scraping and data processing.

Beyond a Gaussian Denoiser: Residual Learning of Deep CNN for Image Denoising (TIP, 2017)

Chromatin immunoprecipitation (ChIP-seq) analysis using BWA and MACS2 with QC steps.

Integrative analysis pipeline for pooled CRISPR functional genetic screens

Web scraping using rvest, httr and Rselenium.

Scripts for processing and predicting CRISPR/Cas9-generated mutations

R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)

Fast Fourier Transform-accelerated Interpolation-based t-SNE (FIt-SNE)

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

Launcher for Windows, an alternative to Alfred and Launchy.

A community Bash framework.

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

Collection of scripts to aggregate image data for the purposes of training an NSFW Image Classifier

MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data.

Outline Manager, developed by Jigsaw. The Outline Manager application creates and manages Outline servers, powered by Shadowsocks. It uses the Electron framework to offer support for Windows, macOS…

Command-line program to download videos from YouTube.com and other video sites

《动手学深度学习》，英文版即伯克利深度学习（STAT 157，2019春）教材。面向中文读者、能运行、可讨论。

深度学习教程整理 | 干货

Curated list of project-based tutorials

A Stable & Secure Tunnel Based On KCP with N:M Multiplexing