sunqiangzai

CGRS

We established a new prognostic signature, clinic and genetic risk score (CGRS), by integrating gene expression profiles with clinical characteristics. CGRS has been confirmed in four different cohorts for accurately predicting GC prognosis, and significantly stratified stage III GC patients into high and low risk groups with different survival time. Furthermore, an easy-to-use nomogram and web application based on CGRS were developed to facilitate its application in clinical practice.

ENCODE_miRNA_pipeline

fastp

A FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...)

GeneFuse

Gene fusion detection and visualization

maftools

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

MetDNA

All the source code of MetDNA.

NeoPredPipe

Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.

speedseq

A flexible framework for rapid genome analysis and interpretation

SURVIV

Survival Analysis of mRNA Isoform Variation

sunqiangzai/AEG_Proteomics

sunqiangzai/alphafold_non_docker

AlphaFold2 non-docker setup

sunqiangzai/AssemblyBasedHaplotypeResolution

Haplotype resolve epigenetic and transcriptomic data types

sunqiangzai/CancerAPA

Cancer susceptible genes revealed by transcriptome-wide association study

sunqiangzai/Chinese-Pangenome-Consortium-Phase-I

sunqiangzai/CHIP-mutation-calling-NGS-pipeline

This pipeline based on snakemake calls CHIP variants from next-generation whole-exome/genome sequencing of human samples and produces a purely filtered VCF file containing high confident CHIP mutations.

sunqiangzai/ChromoDethripsis

Haplotype resolution of chromothriptic and rearranged chromosomes

sunqiangzai/ChromothripsisPaperFigures

Scripts to produce custom figures for the chromothripsis paper

sunqiangzai/CN1

The complete sequence of a Chinese individual

sunqiangzai/CPC-graph-based-NGS-pipeline

A graph-based pipeline used to call/genotype snvs/indels/SVs from NGS data

sunqiangzai/DaPars2

Dynamics analysis of Alternative PolyAdenylation from RNA-seq

sunqiangzai/Deep_KsuccSite

Deep learning models for predicting Succinylation

sunqiangzai/DLm6Am

DLm6Am

sunqiangzai/EasyAmplicon

Easy Amplicon data analysis pipeline

sunqiangzai/EasyMetagenome

Easy Metagenome Pipeline

sunqiangzai/HiFi-human-WGS-WDL

sunqiangzai/HiFiAdapterFilt

Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).

sunqiangzai/HMA

Human Muscle Ageing Cell Atlas

sunqiangzai/hmftools

Various algorithms for analysing genomics data

sunqiangzai/Hotspot

sunqiangzai/humanT2TPhasedGenome

sunqiangzai/NanoMUD

sunqiangzai/neoadjuvant-therapy-response-predictor

sunqiangzai/nnDetection

nnDetection is a self-configuring framework for 3D (volumetric) medical object detection which can be applied to new data sets without manual intervention. It includes guides for 12 data sets that were used to develop and evaluate the performance of the proposed method.

sunqiangzai/ont_m6a_detection

sunqiangzai/PTC_multi_omics

Multi omics integration analysis of papillary thyroid cancer

sunqiangzai/rna_seq_ovcan

Code for Cook et al., Communications Biology, 2023

sunqiangzai/seGMM

A new tool to infer sex from massively parallel sequencing data.

sunqiangzai/slow5tools

Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.

sunqiangzai/SQANTI3

Tool for the Quality Control of Long-Read Defined Transcriptomes