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
Pipeline status
1
active
Pipeline groups
1
A short overview of the main analysis steps for eQTL Catalogue
1
ATAC-seq Pipeline (ENCODE replicated)
1
ATAC-seq Pipeline (ENCODE unreplicated)
1
ATAC-seq Pipeline Cebola Lab
1
ATAC-seq Pipeline Cebola Lab (Hepatocytes)
1
ATAC-seq Pipeline Gaulton Lab
1
ATAC-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
1
Activity by Contact
1
Annotation pipeline popularVote (popV for short) from Tabula Sapiens
1
ChIP-Atlas Pipeline
1
ChIP-seq Pipeline (ENCODE)
1
ChIP-seq Pipeline Cebola Lab
1
ChIP-seq Pipeline Ellinor Lab
1
DNase-seq Pipeline (ENCODE)
1
Histone ChIP-seq Pipeline 2 (ENCODE replicated)
1
Histone ChIP-seq Pipeline 2 (ENCODE unreplicated)
1
Pipeline holder for unknown or undefined pipeline
1
Pseudo-bulk gene expression and differential activity (Elgamal et al.)
1
RNA-seq Pipeline (Paired-ended, ENCODE)
1
RNA-seq Pipeline (Single-ended, ENCODE)
1
RNA-seq Pipeline 2 (Paired-ended, ENCODE)
1
RNA-seq Pipeline 2 (Single-ended, ENCODE)
1
RNA-seq Pipeline Cebola Lab
1
RNA-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
1
TF ChIP-seq Pipeline 2 (ENCODE replicated)
1
TF ChIP-seq Pipeline 2 (ENCODE unreplicated)
1
scRNA-seq clustering for HPAP dataset
Software
1
BEDTools
1
Bowtie 2
1
Irreproducible Discovery Rate (IDR)
1
MACS2
1
Phantompeakqualtools
1
Picard
1
Samtools
1
bedToBigBed
1
cutadapt
1
overlap_peaks.py
1
sambamba
Developed by
1
AMP-T2D consortium
Showing 1 of 1 results
table-tab-icon
matrix-icon
Pipeline
DPL707AXE
active
ATAC-seq Pipeline (ENCODE replicated)
Assays:
ATAC-seq
Software:
Bowtie 2, Samtools, Picard, cutadapt, sambamba, overlap_peaks.py, bedToBigBed, Irreproducible Discovery Rate (IDR), BEDTools, MACS2, Phantompeakqualtools