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
Pipeline status
2
active
Pipeline groups
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
ChIP-Atlas Pipeline
1
ChIP-seq Pipeline (ENCODE)
1
ChIP-seq Pipeline Cebola Lab
1
Histone ChIP-seq Pipeline 2 (ENCODE replicated)
1
Histone ChIP-seq Pipeline 2 (ENCODE unreplicated)
1
RNA-seq Pipeline 2 (Paired-ended, ENCODE)
1
RNA-seq Pipeline 2 (Single-ended, ENCODE)
1
TF ChIP-seq Pipeline 2 (ENCODE replicated)
1
TF ChIP-seq Pipeline 2 (ENCODE unreplicated)
Software
2
BEDTools
2
Bowtie 2
2
MACS2
2
Picard
2
Samtools
2
bedToBigBed
2
cutadapt
2
overlap_peaks.py
2
sambamba
1
Irreproducible Discovery Rate (IDR)
0
lrna-index-rsem
Developed by
2
AMP-T2D consortium
Showing 2 of 2 results
table-tab-icon
matrix-icon
Pipeline
DPL403RWM
active
ChIP-seq Pipeline (ENCODE)
Assays:
ChIP-seq
Software:
Bowtie 2, Samtools, sambamba, Picard, cutadapt, MACS2, BEDTools, overlap_peaks.py, bedToBigBed
Pipeline
DPL967MZM
active
ATAC-seq Pipeline (ENCODE unreplicated)
Assays:
ATAC-seq
Software:
Bowtie 2, Samtools, Picard, cutadapt, sambamba, Irreproducible Discovery Rate (IDR), overlap_peaks.py, MACS2, BEDTools, bedToBigBed