Pinned Repositories
ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
ATAC-seq
atac-seq-pipeline
ENCODE ATAC-seq pipeline
awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
BayesPrism
A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
CellOracle
This is the alpha version of the CellOracle package
ChIP-seq-analysis
ChIP-seq analysis notes from Ming Tang
CNVnator
a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
OA-eQTL
code used for OA-eQTL our project
RNA-seq-data-analysis
this is a example of RNA-seq data analysis workflow
tianwen0003's Repositories
tianwen0003/OA-eQTL
code used for OA-eQTL our project
tianwen0003/ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
tianwen0003/BayesPrism
A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
tianwen0003/CellOracle
This is the alpha version of the CellOracle package
tianwen0003/coloc
Repo for the R package coloc
tianwen0003/dap
software package for integrative genetic association analysis
tianwen0003/deepclip
This repository contains all DeepCLIP Python code
tianwen0003/ensembl-vep
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
tianwen0003/eQTac
The eQTac method
tianwen0003/etwas
epigenetic element-based transcriptome-wide association studies (ETWAS)
tianwen0003/gtex-pipeline
GTEx & TOPMed data production and analysis pipelines
tianwen0003/leafcutter
Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
tianwen0003/mashr
An R package for multivariate adaptive shrinkage.
tianwen0003/MuSiC
Multi-subject Single Cell Deconvolution
tianwen0003/postgap
Linking GWAS studies to genes through cis-regulatory datasets
tianwen0003/QBiC-Pred
Quantitative Binding Change Prediction
tianwen0003/qtltools
A complete tool set for molecular QTL discovery and analysis
tianwen0003/rareGWAMA
TESLA implementation (part of rareGWAMA)
tianwen0003/scRNAseq-GBM
tianwen0003/SNPsplit
Allele-specific alignment sorting
tianwen0003/sos
SoS workflow system for daily data analysis
tianwen0003/sqtlseeker2-nf
An automated sQTL mapping pipeline using Nextflow
tianwen0003/stratAS
🌓 Allele specific analyses across cell states and conditions
tianwen0003/sum-stats-formatter
A generic and scaleable GWAS summary statistics table formatter
tianwen0003/susieR
R package for "sum of single effects" regression.
tianwen0003/tensorqtl
Ultrafast GPU-based QTL mapper
tianwen0003/TF-eQTL
tianwen0003/tianwen0003
tianwen0003/TOBIAS
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
tianwen0003/trackplot
trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.