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Assay
9
ChIP-seq
7
ATAC-seq
7
RNA-seq
4
Mint-ChIP-seq
3
DNase-seq
2
single cell isolation followed by RNA-seq
1
whole genome sequencing assay
Pipeline status
27
active
Pipeline groups
1
A short overview of the main analysis steps for eQTL Catalogue
1
ATAC-seq Pipeline (ENCODE replicated)
1
ATAC-seq Pipeline (ENCODE unreplicated)
1
ATAC-seq Pipeline Cebola Lab
ATAC-seq Pipeline Cebola Lab (Hepatocytes)
1
ATAC-seq Pipeline Gaulton Lab
1
ATAC-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
1
Activity by Contact
1
Annotation pipeline popularVote (popV for short) from Tabula Sapiens
1
ChIP-Atlas Pipeline
1
ChIP-seq Pipeline (ENCODE)
1
ChIP-seq Pipeline Cebola Lab
1
ChIP-seq Pipeline Ellinor Lab
1
DNase-seq Pipeline (ENCODE)
1
Histone ChIP-seq Pipeline 2 (ENCODE replicated)
1
Histone ChIP-seq Pipeline 2 (ENCODE unreplicated)
1
Peak Alignment Pipeline
1
Pipeline holder for unknown or undefined pipeline
1
Pseudo-bulk gene expression and differential activity (Elgamal et al.)
1
RNA-seq Pipeline (Paired-ended, ENCODE)
1
RNA-seq Pipeline (Single-ended, ENCODE)
1
RNA-seq Pipeline 2 (Paired-ended, ENCODE)
1
RNA-seq Pipeline 2 (Single-ended, ENCODE)
1
RNA-seq Pipeline Cebola Lab
1
RNA-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
1
TF ChIP-seq Pipeline 2 (ENCODE replicated)
1
TF ChIP-seq Pipeline 2 (ENCODE unreplicated)
1
scRNA-seq clustering for HPAP dataset
Software
16
Samtools
14
MACS2
13
BEDTools
12
Bowtie 2
12
Picard
8
bedToBigBed
8
cutadapt
7
bedGraphToBigWig
7
sambamba
6
STAR
5
RSEM
5
overlap_peaks.py
4
BWA
4
Irreproducible Discovery Rate (IDR)
4
ptools_bin
3
Phantompeakqualtools
3
deepTools
3
fastp
2
Concat-fastq
2
Median Absolute Deviation
2
RNA pipelines
2
TopHat
2
lrna-index-rsem
2
lrna-index-star
2
lrna-index-tophat
2
lrna-mad-qc
2
lrna-quantification
2
lrna-signals
1
Association testing and fine mapping: eQTL-Catalogue/qtlmap
1
BEDOPS
1
ChromHMM
1
CoLo
1
Digital genomic footprinting
1
Gene expression QC and normalisation: eQTL-Catalogue/qcnorm
1
Genotype QC and imputation: eQTL-Catalogue/genimpute
1
Peak alignment
1
RNA-seq quantification: eQTL-Catalogue/rnaseq
1
SALMON
1
SRA_Toolkit
1
Tophat BAM Repair
1
Trim Galore
1
getVariantOverlap.py
1
hotspot2
1
lrna-align-star-pe
1
lrna-align-star-se
1
lrna-align-tophat-pe
1
lrna-align-tophat-se
1
lrna-signals-stranded
1
lrna-signals-unstranded
1
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
1
unknown
Developed by
17
AMP-T2D consortium
6
Kyle Gaulton, UCSD
3
Ines Cebola, Imperial College London
1
Patrick T. Ellinor, Broad
title!
ATAC-seq Pipeline Cebola Lab (Hepatocytes)
type!!!
FileSet
Showing 6 of 27 results
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Pipeline
DPL126DIZ
active
Pipeline holder for unknown or undefined pipeline
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
DPL935TZE
active
TF ChIP-seq Pipeline 2 (ENCODE replicated)
Assays:
ChIP-seq, Mint-ChIP-seq
Software:
Bowtie 2, Samtools, sambamba, Picard, cutadapt, ptools_bin, MACS2, BEDTools, Irreproducible Discovery Rate (IDR), Phantompeakqualtools, bedToBigBed
Pipeline
DPL172PKH
active
RNA-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
Assays:
RNA-seq
Software:
STAR, RSEM
Pipeline
DPL121OYY
active
ATAC-seq Pipeline Gaulton Lab
Assays:
ATAC-seq
Software:
BWA, Samtools, Picard, MACS2, BEDTools
Pipeline
DPL610SXTsingleended
active
RNA-seq Pipeline (Single-ended, ENCODE)
Assays:
RNA-seq
Software:
STAR, RSEM, bedGraphToBigWig