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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

coloc

Repo for the R package coloc

crossmap

Cross-mappability

dap

software package for integrative genetic association analysis

deltasvm

Codes to run deltaSVM models to predict allelic TF binding

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

etwas

epigenetic element-based transcriptome-wide association studies (ETWAS)

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

fastqtl

Enhanced version of the FastQTL QTL mapper

gtex-eqtls

GTEx eQTL analysis

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

hmcan

hmmratac

HMMRATAC peak caller for ATAC-seq data

humankidney_eqtl_and_snatac-seq

codes used in the human kidney eQTL(cf) and eQTL(ci) and snATAC-seq data

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

lily

Detection of super-enhancers in cancer data

macs

MACS -- Model-based Analysis of ChIP-Seq

mashr

An R package for multivariate adaptive shrinkage.

mr-jti

music

Multi-subject Single Cell Deconvolution

oa-eqtl

code used for OA-eQTL our project

pare

PARE: a computational method to Predict Active Regulatory Elements

peer

A factor analysis package