Extended Joint Models for Longitudinal and Survival Data

DISMIR - a deep learning-based cancer-detection method by integrating DNA sequence and methylation information of individual cell-free DNA reads

Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA

Deep Learning Method to Identify Cancer Associated TCRs

Pipeline engine for IDseq (Infectious Disease Sequencing Platform),CZI的病原微生物分析流程

A deep learning-based tool to identify splice variants，剪切位点预测，tensorflow

An open source python library for automated feature engineering，自动化特征生成

Cell Free DNA Sequencing Analysis Pipeline，cfDNA特征提取

Mutational signature analysis for low statistics SNV data，用mutation signature的方式来检测HRD score

Repository for Cibersortx

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

通过LOH+LST+ntAI检测HRD score

肿瘤突变负荷学习笔记（tumor mutation burden）

https://www.cbioportal.org/mutation_mapper，即mutationMapper的react组件，oncoKB和cbioportal都用的这个。

FoundationOne单样本somatic variat caller，用来计算TMB

An excellent pipeline job manager

HLA typing for Sanger Based Test

Graph theory (network) library for visualisation and analysis关系图前端框架

The most trusted Go module proxy in China.

Simple DAG-based job scheduler in Python，DAG可视化，实时预览作业状态。

Detection of micro-satellite instability from circulating tumor DNA by targeted deep sequencing，燃石bMSI检测

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

Generate consensus reads to reduce sequencing noises and remove duplications，寻找UMI下的一致性序列

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

A Java package for non-invasive cancer diagnosis using methylation profiles of cell-Free DNA.

autoencoder to compress methylation data and cancer cell classifier