Pinned Repositories
3Dmol.js
WebGL accelerated JavaScript molecular graphics library
AGFusion
Python package to annotate and visualize gene fusions.
akt
Ancestry and Kinship Tools
cancerTiming
DeepLearning-500-questions
深度学习500问，以问答形式对常用的概率知识、线性代数、机器学习、深度学习、计算机视觉等热点问题进行阐述，以帮助自己及有需要的读者。 全书分为17个章节，20多万字。由于水平有限，书中不妥之处恳请广大读者批评指正。 未完待续............ 如有意合作，联系scutjy2015@163.com 版权所有，违权必究 Tan 2018.06
elasticstack
:card_index: Configurable indexing and other extras for Haystack (with ElasticSearch biases)由于haystack不支持配置elasticsearch的mapping等功能，这个包就是做这个配置的，比如咱们可以支持某个字段用jieba中文分词，另外一个字段用snowball英文分词，非常好。
meth-report-generator
甲基化报告自动化
somatic_pipeline
肿瘤体细胞突变检测流程（组织、cfDNA均可，需要有对照）
wechat_spider
抓取某微信公众号所有历史文章列表及其内容
haoziyeung's Repositories
haoziyeung/wechat_spider
抓取某微信公众号所有历史文章列表及其内容
haoziyeung/autoencoder_for_cancer
autoencoder to compress methylation data and cancer cell classifier
haoziyeung/bMSISEA
Detection of micro-satellite instability from circulating tumor DNA by targeted deep sequencing，燃石bMSI检测
haoziyeung/CancerLocator
A Java package for non-invasive cancer diagnosis using methylation profiles of cell-Free DNA.
haoziyeung/CaVEMan
SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
haoziyeung/cfDNA
Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA
haoziyeung/cfdna_multimodal_patterns
Discovery multi-modal signals captured by fragmentation patterns of cell-free DNA
haoziyeung/cfDNApipe
Cell Free DNA Sequencing Analysis Pipeline，cfDNA特征提取
haoziyeung/Cibersortx
Repository for Cibersortx
haoziyeung/conta
Conta is an R package to detect cross contamination and source of contamination,GRAIL根据informative SNP检测样本间污染的软件
haoziyeung/cow
HTTP proxy written in Go. COW can automatically identify blocked sites and use parent proxies to access.配合ss做二级跳转
haoziyeung/cytoscape.js
Graph theory (network) library for visualisation and analysis关系图前端框架
haoziyeung/dagobah
Simple DAG-based job scheduler in Python，DAG可视化，实时预览作业状态。
haoziyeung/DeepCAT
Deep Learning Method to Identify Cancer Associated TCRs
haoziyeung/DISMIR
DISMIR - a deep learning-based cancer-detection method by integrating DNA sequence and methylation information of individual cell-free DNA reads
haoziyeung/featuretools
An open source python library for automated feature engineering，自动化特征生成
haoziyeung/gencore
Generate consensus reads to reduce sequencing noises and remove duplications，寻找UMI下的一致性序列
haoziyeung/goproxy.cn
The most trusted Go module proxy in China.
haoziyeung/haoziyeung.github.io
my landing page
haoziyeung/idseq-dag
Pipeline engine for IDseq (Infectious Disease Sequencing Platform),CZI的病原微生物分析流程
haoziyeung/JMbayes2
Extended Joint Models for Longitudinal and Survival Data
haoziyeung/react-mutation-mapper
https://www.cbioportal.org/mutation_mapper，即mutationMapper的react组件，oncoKB和cbioportal都用的这个。
haoziyeung/scarHRD
通过LOH+LST+ntAI检测HRD score
haoziyeung/SGZ
FoundationOne单样本somatic variat caller，用来计算TMB
haoziyeung/SigMA
Mutational signature analysis for low statistics SNV data，用mutation signature的方式来检测HRD score
haoziyeung/SJM
An excellent pipeline job manager
haoziyeung/SOAPTyping
HLA typing for Sanger Based Test
haoziyeung/SpliceAI
A deep learning-based tool to identify splice variants，剪切位点预测，tensorflow
haoziyeung/supp_files
attachments for github issues
haoziyeung/TMB
肿瘤突变负荷学习笔记（tumor mutation burden）