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Assay
ATAC-seq
1
ChIP-seq
1
RNA-seq
Pipeline status
2
active
Pipeline groups
1
ChIP-seq Pipeline Cebola Lab
1
RNA-seq Pipeline Cebola Lab
Software
11
Samtools
9
Bowtie 2
8
BEDTools
8
MACS2
7
Picard
6
STAR
6
bedGraphToBigWig
6
bedToBigBed
6
cutadapt
5
RSEM
5
sambamba
4
ptools_bin
3
overlap_peaks.py
2
BWA
2
Concat-fastq
2
Irreproducible Discovery Rate (IDR)
2
Median Absolute Deviation
2
Phantompeakqualtools
2
RNA pipelines
2
TopHat
2
deepTools
2
fastp
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
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
unknown
Developed by
2
Ines Cebola, Imperial College London
assay_term_names!
ATAC-seq
Showing 2 of 2 results
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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