dapeng Liang's repositories
annovar2maf
Tiny python script to generate MAF files from output generated by standard annotation programs
awesome
Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.
awesome_spatial_omics
tools and notes for spatial omics
data_analysis
Streamline a data analysis process
drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
EasyMicrobiomeR
Using R language in microbiome analysis
FRASER
FRASER - Find RAre Splicing Events in RNA-seq
Kubota_puQTL
Codes used in puQTL manuscript
LPRI
LPRI: A workflow for lung cancer patients' stratification
Neoantigen_Pipeline
This repository contains code to identify potential neoantigens from RNA-Seq data based on the splicing profile of User-Provided Tumor Samples
OINC-seq
oxidation induced nucleotide conversions
PTC_multi_omics
Multi omics integration analysis of papillary thyroid cancer
reprocess_public_10x
Scripts to help get fastqs
scPagwas
Obtain trait-relevant cell subpopulations by incorporating pathway activity transformed scRNA-seq data with GWAS data
single-cell-papers-with-code
Papers with code for single cell related papers
SituSeq
workflows for offline analysis of 16S rRNA Nanopore data
SPAGEfinder
Computational approach to identify Survival associated Pairwise Gene Expression states.
sports1.1
Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
SSNIP
The Spatial Splicing-derived Neoantigen Identifier Pipeline (SSNIP) allows for the precise characterization of neoantigens derived from cancer-specific splicing events (neojunctions). The code available in this repository are the neopeptide identifier stages: 1. Neojunction calling, 2. Neopeptide prediction, 3. n-mer presentation prediction
STARsolo
wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
TwoSampleMR_pipeline
Pipeline that runs two-sample Mendelian randomization on molecular QTLs and GWAS loci and tests for horizontal pleiotropy.
xQTLbiolinks
xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs