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Assay
2
ChIP-seq
2
DNase-seq
1
ATAC-seq
1
RNA-seq
1
single cell isolation followed by RNA-seq
1
whole genome sequencing assay
Pipeline status
4
active
Pipeline groups
1
A short overview of the main analysis steps for eQTL Catalogue
1
Activity by Contact
1
ChIP-Atlas Pipeline
1
Pseudo-bulk gene expression and differential activity (Elgamal et al.)
Software
2
BEDTools
2
MACS2
1
Association testing and fine mapping: eQTL-Catalogue/qtlmap
1
Bowtie 2
1
CoLo
1
Gene expression QC and normalisation: eQTL-Catalogue/qcnorm
1
Genotype QC and imputation: eQTL-Catalogue/genimpute
1
RNA-seq quantification: eQTL-Catalogue/rnaseq
1
SRA_Toolkit
1
Samtools
1
bedGraphToBigWig
1
getVariantOverlap.py
1
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
1
unknown
Developed by
3
AMP-T2D consortium
1
Kyle Gaulton, UCSD
Showing 4 of 4 results
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Pipeline
DPL066WNI
active
Pseudo-bulk gene expression and differential activity (Elgamal et al.)
Assays:
single cell isolation followed by RNA-seq
Pipeline
DPL005RCG
active
A short overview of the main analysis steps for eQTL Catalogue
Assays:
RNA-seq, whole genome sequencing assay
Software:
RNA-seq quantification: eQTL-Catalogue/rnaseq, Gene expression QC and normalisation: eQTL-Catalogue/qcnorm, Genotype QC and imputation: eQTL-Catalogue/genimpute, Association testing and fine mapping: eQTL-Catalogue/qtlmap
Pipeline
DPL983WYV
active
ChIP-Atlas Pipeline
Assays:
ChIP-seq, DNase-seq
Software:
SRA_Toolkit, Bowtie 2, Samtools, BEDTools, bedGraphToBigWig, MACS2, unknown, CoLo
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