lybird300

methylpy

WGBS/NOMe-seq Data Processing & Differential Methylation Analysis

DIALOGUE

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.

rGREAT

GREAT Analysis - Functional Enrichment on Genomic Regions

ImmuneResistance

This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources of T cell exclusion linked to immunotherapy clinical outcomes".

LOLA

Locus Overlap Analysis: Enrichment of Genomic Ranges

scWGCNA

scWGCNA

scgenetics

identifying disease critical cell types and programs from single cell RNAseq

GSSG

Gene Set + S2G strategy annotations analyzed for disease architecture

PanCancer

Data available at: https://www.dropbox.com/sh/jh4s57kgbb0rnxe/AABoMK466cGc1OKsOuFN10wca?dl=0 and https://nyulangone-my.sharepoint.com/:f:/g/personal/dalia_barkley_nyulangone_org/EuHetdAOc2pLjm9XUwqdWicBnlXIbyvHx-EOC-inP-SGUg?e=rxa7Ry

ENCODE-cCREs

Pipelines to create and analyze ENCODE candidate cis-Regulatory Elements

immucan-scdb

eGTEx_mQTLs_eQTLs_GWAS

encode_dna_dynamics

Custom scripts used in "Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus"

CAMDA

Quantify the Concurrence of DNA Methylation and De-methylation

msfs_teo

mSFS using a teosinte natural population

DCATS

colon-dna-topology

spiromics-covid19-eqtl

Mapping of cis-eQTLs for COVID-19-related genes in the SPIROMICS dataset

metabric_rrbs

MethSig

scRNAseq_comparison_vignette

Tutorial of condition comparison analysis of scRNA-seq data

downstream-QTL

set of scripts and pipelines to work with QTL results

Fine-mapping_SCARB2_CTSB

PDX-PanCanAtlas

HirstLab

Code and results in Hirst Lab

scRNA_Seq-Differential_Variability_Analysis

Mallm-et-al-processing-scripts

A public repository to reproduce data processing and analysis for Mallm, Iskar, Ishaque et. al. 2018

EAC_GBM_comparative_epigenomics

This is the repository for all code pertaining to the manuscript "Comparative epigenomics between distinct cancer types reveals common trends behind cancer DNA methylation abnormalities"

cardiac_eqtls

Cardiac eQTL analysis

RAMPAGE-Analysis