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/akt
Ancestry and Kinship Tools
haoziyeung/battenberg
Battenberg R package for subclonal copynumber estimation
haoziyeung/clonevol
Inferring and visualizing clonal evolution in multi-sample cancer sequencing
haoziyeung/CutePeaks
A simple viewer for Sanger file
haoziyeung/EAGLE
Enhanced Artificial Genome Engine: next generation sequencing reads simulator
haoziyeung/giggle
Interval data structure一个做基因组数据库搜索的，有点像bedtools...
haoziyeung/gitbook
haoziyeung/hap.py
Haplotype VCF comparison tools比较咱们call出来的vcf和gold standard（例如giab）的差别，用于评判自己的pipeline的好坏
haoziyeung/HLAminer
HLA predictions from NGS shotgun data
haoziyeung/IGV-snapshot-automator
Script to automatically create and run IGV snapshot batchscripts
haoziyeung/INTEGRATE-Neo
基因融合新抗原预测
haoziyeung/learning_bam_file
Learning the Sequence Alignment/Map format
haoziyeung/MutationTime.R
An R script to time somatic mutations
haoziyeung/NGSCheckMate
Software program for checking sample matching for NGS data检查两个数据是否来自于同一个样本
haoziyeung/oncokb-annotator
Annotates variants in MAF with OncoKB annotation.这个软件是MSK做的，用来注释他们出的那个oncokb数据库
haoziyeung/pcgr
Personal Cancer Genome Reporter (PCGR)肿瘤报告自动化解决方案
haoziyeung/pedigreejs
A web tool for building pedigrees, https://ccge-boadicea.github.io/pedigreejs/，一个做家系图的js插件
haoziyeung/phylowgs
Application for inferring subclonal composition and evolution from whole-genome sequencing data.
haoziyeung/plenv
Perl binary manager一个perl多版本管理工具
haoziyeung/pyauto
《python自动化运维：技术与最佳实践》书中示例及案例源码
haoziyeung/pyclone
Probabilistic model for inferring clonal population structure from deep NGS sequencing.肿瘤亚克隆-进化分析,可以配合Sequenza用
haoziyeung/pyensembl
Python interface to ensembl reference genome metadata (exons, transcripts, etc...)
haoziyeung/seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
haoziyeung/TitanCNA
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer,PhyloWGS 的CNV输入来源，由于Battenberg会产生海量（千万级）的中间文件，而且不好安装，不好使用，因此这个可以考虑
haoziyeung/tredparse
TREDPARSE: HLI Short Tandem Repeat (STR) caller
haoziyeung/TS
Torrent Suite
haoziyeung/varsim
VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications，可以模拟fastq文件，这样就能跑完整的流程了，bamsurgeon只能模拟bam文件
haoziyeung/vcflib
a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
haoziyeung/VerifyBamID
A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
haoziyeung/zTree_v3
jQuery Tree Plugin