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Assay
RNA-seq
2
ATAC-seq
2
ChIP-seq
1
DNase-seq
Pipeline status
4
active
Pipeline groups
1
ATAC-seq Pipeline Cebola Lab
1
ATAC-seq Pipeline Cebola Lab (Hepatocytes)
1
ChIP-Atlas Pipeline
1
ChIP-seq Pipeline Cebola Lab
Software
15
MACS2
14
BEDTools
14
Samtools
12
Picard
11
Bowtie 2
8
bedToBigBed
8
cutadapt
7
sambamba
5
overlap_peaks.py
4
BWA
4
Irreproducible Discovery Rate (IDR)
4
bedGraphToBigWig
4
ptools_bin
3
Phantompeakqualtools
3
deepTools
3
fastp
1
BEDOPS
1
ChromHMM
1
CoLo
1
Digital genomic footprinting
1
SRA_Toolkit
1
Trim Galore
1
getVariantOverlap.py
1
hotspot2
1
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
1
unknown
Developed by
3
Ines Cebola, Imperial College London
1
AMP-T2D consortium
assay_term_names!
RNA-seq
Showing 4 of 4 results
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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
DPL741HGX
active
ATAC-seq Pipeline Cebola Lab
Assays:
ATAC-seq
Software:
fastp, Bowtie 2, Samtools, Picard, BEDTools, deepTools, MACS2, bedGraphToBigWig
Pipeline
DPL245EPK
active
ChIP-seq Pipeline Cebola Lab
Assays:
ChIP-seq
Software:
fastp, Bowtie 2, Samtools, BEDTools, deepTools, MACS2, bedGraphToBigWig
Pipeline
DPL983WYV
active
ChIP-Atlas Pipeline
Assays:
ChIP-seq, DNase-seq
Software:
SRA_Toolkit, Bowtie 2, Samtools, BEDTools, bedGraphToBigWig, MACS2, unknown, CoLo