Pinned Repositories
AC-ICAM-NM
Code related to the 2023 AC-ICAM manuscript in Nature Medicine.
agilent
Microarray analysis of agilent data
AIPS
Absolute Inference of Patient Signatures
Alternative-Splicing-Tools
A list of alternative splicing analysis resources
aneuploidy_score
R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al. (https://doi.org/10.1038/s41467-020-14286-0)
annoPeak
APAsurvey
A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data
CASE_splicing
RNAMod
Sierra
Discover differential transcript usage from polyA-captured single cell RNA-seq data
liangdp1984's Repositories
liangdp1984/annovar2maf
Tiny python script to generate MAF files from output generated by standard annotation programs
liangdp1984/awesome
Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.
liangdp1984/awesome-riboseq
A list of bioinformatic tools for working with Ribo-Seq data
liangdp1984/awesome_spatial_omics
tools and notes for spatial omics
liangdp1984/bulkPseudotime
Pseudotime Analysis for Bulk Data
liangdp1984/CSI-Microbes-identification
Code for the identification step for CSI-Microbes
liangdp1984/data_analysis
Streamline a data analysis process
liangdp1984/drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
liangdp1984/ESCA_WGBS_analysis
liangdp1984/hpgltools
A collection of R functions to aid in host-pathogen genomic research
liangdp1984/immunotar
liangdp1984/Kubota_puQTL
Codes used in puQTL manuscript
liangdp1984/LPRI
LPRI: A workflow for lung cancer patients' stratification
liangdp1984/melanoma_PScore
liangdp1984/microbiome_reconstruction
liangdp1984/Neoantigen_Pipeline
This repository contains code to identify potential neoantigens from RNA-Seq data based on the splicing profile of User-Provided Tumor Samples
liangdp1984/OINC-seq
oxidation induced nucleotide conversions
liangdp1984/omnideconv
liangdp1984/ONT-LR-seq-in-HVSMC
liangdp1984/pig-omics-project
liangdp1984/PTC_multi_omics
Multi omics integration analysis of papillary thyroid cancer
liangdp1984/reprocess_public_10x
Scripts to help get fastqs
liangdp1984/scPagwas
Obtain trait-relevant cell subpopulations by incorporating pathway activity transformed scRNA-seq data with GWAS data
liangdp1984/SituSeq
workflows for offline analysis of 16S rRNA Nanopore data
liangdp1984/SPAGEfinder
Computational approach to identify Survival associated Pairwise Gene Expression states.
liangdp1984/sports1.1
Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
liangdp1984/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
liangdp1984/STARsolo
wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
liangdp1984/TwoSampleMR_pipeline
Pipeline that runs two-sample Mendelian randomization on molecular QTLs and GWAS loci and tests for horizontal pleiotropy.
liangdp1984/xQTLbiolinks
xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs