Omics Pipe: a community-based framework for reproducible multi-omics data analysis (Q30886785)

26 September 2017

Omics Pipe: a community-based framework for reproducible multi-omics data analysis (English)

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26 September 2017

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7

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PubMed publication ID

27 June 2017

Kathleen M Fisch

1

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Tobias Meißner

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Tobias Meißner

2

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Louis Gioia

3

object named as

Louis Gioia

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26 September 2017

6

Salvatore Loguercio

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26 September 2017

Jean-Christophe Ducom

4

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26 September 2017

Tristan M Carland

5

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26 September 2017

language of work or name

English

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publication date

30 January 2015

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26 September 2017

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26 September 2017

31

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26 September 2017

11

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26 September 2017

1724-1728

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OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

HTSeq--a Python framework to work with high-throughput sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Harnessing virtual machines to simplify next-generation DNA sequencing analysis.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Dysregulation of the basal RNA polymerase transcription apparatus in cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

STAR: ultrafast universal RNA-seq aligner

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Comprehensive molecular portraits of human breast tumours

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

An integrated encyclopedia of DNA elements in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Identifying ChIP-seq enrichment using MACS.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Snakemake--a scalable bioinformatics workflow engine

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Bpipe: a tool for running and managing bioinformatics pipelines

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

graphite - a Bioconductor package to convert pathway topology to gene network.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

A decade's perspective on DNA sequencing technology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Ruffus: a lightweight Python library for computational pipelines

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

A scaling normalization method for differential expression analysis of RNA-seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

A novel signaling pathway impact analysis.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Identification of mRNAs differentially-expressed between benign and malignant breast tumour cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443682

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV061

Automated Capture of Experiment Context for Easier Reproducibility in Computational Research

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTV061

10.1093/BIOINFORMATICS/BTV061

21 January 2018

Identifiers

DOI

1 reference

journals/bioinformatics/FischMGDCLS15

26 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

26 September 2017

PubMed publication ID

25637560

1 reference