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Assay
7
RNA-seq
3
ChIP-seq
2
ATAC-seq
2
DNase-seq
2
single cell isolation followed by RNA-seq
1
whole genome sequencing assay
Pipeline status
2
active
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1
ATAC-seq Pipeline Cebola Lab (Hepatocytes)
1
Activity by Contact
Software
7
MACS2
6
BEDTools
6
Samtools
Picard
4
Bowtie 2
2
BWA
2
Irreproducible Discovery Rate (IDR)
2
bedGraphToBigWig
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bedToBigBed
2
cutadapt
2
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2
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2
overlap_peaks.py
2
sambamba
1
Phantompeakqualtools
1
Trim Galore
1
getVariantOverlap.py
1
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
Developed by
1
AMP-T2D consortium
1
Ines Cebola, Imperial College London
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Picard
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Pipeline
DPL779IGH
active
ATAC-seq Pipeline Cebola Lab (Hepatocytes)
Assays:
ATAC-seq
Software:
fastp, Bowtie 2, Samtools, BEDTools, deepTools, MACS2, bedGraphToBigWig
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