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Assay
8
ChIP-seq
7
RNA-seq
6
ATAC-seq
4
Mint-ChIP-seq
2
DNase-seq
2
single cell isolation followed by RNA-seq
1
whole genome sequencing assay
Pipeline status
2
active
Pipeline groups
1
ChIP-Atlas Pipeline
1
DNase-seq Pipeline (ENCODE)
Software
2
BEDTools
2
MACS2
2
Samtools
1
BEDOPS
1
BWA
1
Bowtie 2
1
CoLo
1
Digital genomic footprinting
1
Picard
1
SRA_Toolkit
1
bedGraphToBigWig
1
bedToBigBed
1
cutadapt
1
getVariantOverlap.py
1
hotspot2
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
1
unknown
Developed by
2
AMP-T2D consortium
analysis_steps.versions.software_versions.software.title!
makeCandidateRegions.py
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Pipeline
DPL930NXT
active
DNase-seq Pipeline (ENCODE)
Assays:
DNase-seq
Software:
hotspot2, BEDOPS, BWA, cutadapt, Samtools, Picard, Digital genomic footprinting, bedToBigBed
Pipeline
DPL983WYV
active
ChIP-Atlas Pipeline
Assays:
ChIP-seq, DNase-seq
Software:
SRA_Toolkit, Bowtie 2, Samtools, BEDTools, bedGraphToBigWig, MACS2, unknown, CoLo