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Assay
3
RNA-seq
2
ChIP-seq
1
ATAC-seq
1
DNase-seq
1
single cell isolation followed by RNA-seq
1
whole genome sequencing assay
Pipeline status
7
active
Pipeline groups
1
A short overview of the main analysis steps for eQTL Catalogue
1
Activity by Contact
1
Annotation pipeline popularVote (popV for short) from Tabula Sapiens
1
ChIP-seq Pipeline Ellinor Lab
1
Pipeline holder for unknown or undefined pipeline
1
RNA-seq Pipeline (Paired-ended, ENCODE)
1
RNA-seq Pipeline (Single-ended, ENCODE)
Software
Samtools
13
BEDTools
13
Bowtie 2
13
MACS2
10
Picard
8
bedGraphToBigWig
8
bedToBigBed
8
cutadapt
7
sambamba
5
STAR
5
overlap_peaks.py
4
Irreproducible Discovery Rate (IDR)
4
RSEM
4
deepTools
4
fastp
4
ptools_bin
3
Phantompeakqualtools
2
BWA
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
RNA-seq quantification: eQTL-Catalogue/rnaseq
1
SALMON
1
SRA_Toolkit
1
Tophat BAM Repair
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
6
AMP-T2D consortium
Kyle Gaulton, UCSD
1
Patrick T. Ellinor, Broad
analysis_steps.versions.software_versions.software.title!
Samtools
lab.title!
Kyle Gaulton, UCSD
Showing 7 of 7 results
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Pipeline
DPL472KCS
active
Annotation pipeline popularVote (popV for short) from Tabula Sapiens
Assays:
single cell isolation followed by RNA-seq
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
DPL118KGX
active
ChIP-seq Pipeline Ellinor Lab
Assays:
ChIP-seq
Software:
BWA, Picard, MACS2, BEDTools, ChromHMM
Pipeline
DPL610SXT
active
RNA-seq Pipeline (Paired-ended, ENCODE)
Assays:
RNA-seq
Software:
STAR, bedGraphToBigWig, RSEM
Pipeline
DPL610SXTsingleended
active
RNA-seq Pipeline (Single-ended, ENCODE)
Assays:
RNA-seq
Software:
STAR, RSEM, 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