sunqiangzai's repositories
alphafold_non_docker
AlphaFold2 non-docker setup
AssemblyBasedHaplotypeResolution
Haplotype resolve epigenetic and transcriptomic data types
CancerAPA
Cancer susceptible genes revealed by transcriptome-wide association study
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.
ChromoDethripsis
Haplotype resolution of chromothriptic and rearranged chromosomes
ChromothripsisPaperFigures
Scripts to produce custom figures for the chromothripsis paper
CN1
The complete sequence of a Chinese individual
CPC-graph-based-NGS-pipeline
A graph-based pipeline used to call/genotype snvs/indels/SVs from NGS data
DaPars2
Dynamics analysis of Alternative PolyAdenylation from RNA-seq
Deep_KsuccSite
Deep learning models for predicting Succinylation
DLm6Am
DLm6Am
EasyAmplicon
Easy Amplicon data analysis pipeline
EasyMetagenome
Easy Metagenome Pipeline
HiFiAdapterFilt
Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
HMA
Human Muscle Ageing Cell Atlas
hmftools
Various algorithms for analysing genomics data
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.
PTC_multi_omics
Multi omics integration analysis of papillary thyroid cancer
rna_seq_ovcan
Code for Cook et al., Communications Biology, 2023
seGMM
A new tool to infer sex from massively parallel sequencing data.
slow5tools
Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.
SQANTI3
Tool for the Quality Control of Long-Read Defined Transcriptomes