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杨浩's Projects

react-mutation-mapper icon react-mutation-mapper

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

reportit icon reportit

IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results.IonTorrent自动报告系统

rnaseq_tutorial icon rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

safeseqs icon safeseqs

Python pipeline for analysis of SafeSeqS DNA sequencing data. UMI处理

samplot icon samplot

Plot structural variant signals from many BAMs and CRAMs

sanefalcon icon sanefalcon

SANEFALCON (Single reAds Nucleosome-basEd FetAL fraCtiON): Calculating the fetal fraction for noninvasive prenatal testing based on genome-wide nucleosome profiles.通过核小体，计算胎源比例。

sangeranalyser icon sangeranalyser

functions to analyse sanger sequencing reads in R分析AB1文件，非常强大

scout icon scout

VCF visualization interface这个是做vcf可视化交互分析的

seqff icon seqff

Python Implementation of SeqFF for Fetal Fraction Calculation using Elastic Net

seqkit icon seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

sgz icon sgz

FoundationOne单样本somatic variat caller，用来计算TMB

sigma icon sigma

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

sjm icon sjm

An excellent pipeline job manager

soapdenovo2 icon soapdenovo2

Next generation sequencing reads de novo assembler.

somatic_pipeline icon somatic_pipeline

肿瘤体细胞突变检测流程（组织、cfDNA均可，需要有对照）

spliceai icon spliceai

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

strelka icon strelka

Strelka2 germline and somatic small variant caller这个对高深度的，例如组织的somatic突变，检出率挺好，并且运行速度很快

surpi icon surpi

computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data.

svglib icon svglib

Read SVG files and convert them to other formats (moved to here from https://bitbucket.org/deeplook/svglib).python处理svg的模块，可以将svg转换为png或者pdf

svviz icon svviz

Read visualizer for structural variants

taxmaps icon taxmaps

Ultra-efficient taxonomic mapping of NGS data

telseq icon telseq

A software for calculating telomere length统计端粒长度，相比MotifCounter、Computel、qMotif、Telomerecat更加易用

textract icon textract

extract text from any document. no muss. no fuss.利用python可以读取pdf里面的内容，接下来就可以用hystack做全文检索了

thapmix icon thapmix

Haplotype-based somatic genome simulator

theta icon theta

Tumor Heterogeneity Analysis (THetA) is an algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. Please note that the latest release is now called THetA2.也可以做肿瘤纯度分析,并且支持WXS，比ABSOLUTE范围广一些，而且发表日期更新一些，不过ABS是发在NG上的...

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