Search – Common Metabolic Diseases Genome Atlas

Showing 18 of 26 results

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Pipeline
DPL857456
active
Peak Alignment Pipeline
Assays: ATAC-seq
Software: Peak alignment
Pipeline
DPL255HPT
active
scRNA-seq clustering for HPAP dataset
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
DPL721SCW
active
Histone ChIP-seq Pipeline 2 (ENCODE unreplicated)
Assays: ChIP-seq, Mint-ChIP-seq
Software: Bowtie 2, Samtools, sambamba, Picard, cutadapt, ptools_bin, overlap_peaks.py, bedToBigBed, MACS2, BEDTools
Pipeline
DPL961ZQY
active
ATAC-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
Assays: ATAC-seq
Software: Trim Galore, BWA, Samtools, Picard, MACS2
Pipeline
DPL172PKH
active
RNA-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
Assays: RNA-seq
Software: STAR, RSEM
Pipeline
DPL930NXT
active
DNase-seq Pipeline (ENCODE)
Assays: DNase-seq
Software: hotspot2, BEDOPS, BWA, cutadapt, Samtools, Picard, Digital genomic footprinting, bedToBigBed
Pipeline
DPL064PJG
active
Histone ChIP-seq Pipeline 2 (ENCODE replicated)
Assays: ChIP-seq, Mint-ChIP-seq
Software: Bowtie 2, Samtools, sambamba, cutadapt, Picard, ptools_bin, MACS2, BEDTools, overlap_peaks.py, bedToBigBed
Pipeline
DPL121OYY
active
ATAC-seq Pipeline Gaulton Lab
Assays: ATAC-seq
Software: BWA, Samtools, Picard, MACS2, BEDTools
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
DPL450NWL
active
RNA-seq Pipeline Cebola Lab
Assays: RNA-seq
Software: fastp, STAR, SALMON, Samtools, deepTools
Pipeline
DPL245EPK
active
ChIP-seq Pipeline Cebola Lab
Assays: ChIP-seq
Software: fastp, Bowtie 2, Samtools, BEDTools, deepTools, MACS2, bedGraphToBigWig
Pipeline
DPL403RWM
active
ChIP-seq Pipeline (ENCODE)
Assays: ChIP-seq
Software: Bowtie 2, Samtools, sambamba, Picard, cutadapt, MACS2, BEDTools, overlap_peaks.py, bedToBigBed
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

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Showing 18 of 26 results