Toggle navigation
Home
About
Project overview
Policies
News
Contact
Data
Experiments
Annotations
Single Cell Embeddings
Statistical Models
Gene Perturbations
Data Standards & QC
Pipelines
Consortia
Publications
Tools
Single Cell Browser
Help
Getting started
Schema
Clear Filters
Assay
1
ATAC-seq
1
ChIP-seq
1
DNase-seq
1
RNA-seq
1
single cell isolation followed by RNA-seq
1
whole genome sequencing assay
Pipeline status
3
active
Pipeline groups
1
A short overview of the main analysis steps for eQTL Catalogue
1
Activity by Contact
ChIP-Atlas Pipeline
1
Pseudo-bulk gene expression and differential activity (Elgamal et al.)
Software
1
Association testing and fine mapping: eQTL-Catalogue/qtlmap
1
BEDTools
1
Gene expression QC and normalisation: eQTL-Catalogue/qcnorm
1
Genotype QC and imputation: eQTL-Catalogue/genimpute
1
MACS2
1
RNA-seq quantification: eQTL-Catalogue/rnaseq
1
getVariantOverlap.py
1
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
Developed by
2
AMP-T2D consortium
1
Kyle Gaulton, UCSD
title!
ChIP-Atlas Pipeline
Showing 3 of 3 results
table-tab-icon
matrix-icon
Pipeline
DPL066WNI
active
Pseudo-bulk gene expression and differential activity (Elgamal et al.)
Assays:
single cell isolation followed by RNA-seq
Pipeline
DPL005RCG
active
A short overview of the main analysis steps for eQTL Catalogue
Assays:
RNA-seq, whole genome sequencing assay
Software:
RNA-seq quantification: eQTL-Catalogue/rnaseq, Gene expression QC and normalisation: eQTL-Catalogue/qcnorm, Genotype QC and imputation: eQTL-Catalogue/genimpute, Association testing and fine mapping: eQTL-Catalogue/qtlmap
Pipeline
DPL010CNP
active
Activity by Contact
Assays:
ATAC-seq, ChIP-seq, DNase-seq
Software:
MACS2, BEDTools, makeCandidateRegions.py, run.neighborhoods.py, predict.py, getVariantOverlap.py