Pinned Repositories
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's Repositories
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