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/SURVIV
Survival Analysis of mRNA Isoform Variation
sunqiangzai/361Division
361 Division - Scientific Training, Education and Learning
sunqiangzai/awesome-bioinformatics
A curated list of awesome Bioinformatics databases, softwares, libraries, toolboxes, pipelines, books, courses, tutorials and more.
sunqiangzai/Books
无它术，唯勤读书而多为之，自工
sunqiangzai/CIRCexplorer
A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147)
sunqiangzai/course_Bioinformatics
天津医科大学，生物医学工程与技术学院，《生物信息学》课程资料
sunqiangzai/course_Linux
天津医科大学，生物医学工程与技术学院，《Linux系统概论》课程资料
sunqiangzai/curatedBreastCancer
15 studies encompassing 24 different datasets (matrices) from GEO breast cancer gene expression experiments. Treatment information and outcomes data is also curated for each patient (datasets were carefully chosen based upon whether I could determine each sample/patient's treatment regimen, and whether the samples had at least one outcomes variable measured.) This totals over 2700 samples all together from large-scale studies and clinical trials. These datasets are available as an R package, curatedBreastData.
sunqiangzai/DataScienceResources
Open Source Data Science Resources.
sunqiangzai/DREAM-Gene-Essentiality-Challenge
sunqiangzai/echarts
A powerful, interactive charting and visualization library for browser
sunqiangzai/EpiDISH
This package contains a reference-based function to infer the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.
sunqiangzai/forum
蓝灯(Lantern)官方论坛
sunqiangzai/illumina-450K-analysis
From IDAT to beta.
sunqiangzai/Immunophenogram
sunqiangzai/InfiniumPurify
:exclamation: This is a read-only mirror of the CRAN R package repository. InfiniumPurify — Estimate and Account for Tumor Purity in Cancer Methylation Data Analysis
sunqiangzai/knowledge
concepts about methylation
sunqiangzai/Learn-Bioinformatics
sunqiangzai/MCPcounter
sunqiangzai/mutationalProfiles
sunqiangzai/onco_lnc
sunqiangzai/python
番号图
sunqiangzai/RBSSeqTools
sunqiangzai/RiA2
Source code for R in Action, Second Edition
sunqiangzai/RiskNetwork
Risk Network Modeling and Analysis
sunqiangzai/RNAseqDB
sunqiangzai/SC3-paper-figures
Scripts to recreate figures from the SC3 paper
sunqiangzai/scripts4education
教学相关的程序和脚本
sunqiangzai/standard-RAxML
sunqiangzai/zhao
【编程随想】整理的《太子党关系网络》，专门揭露赵国的权贵