Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions

INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments

(2015) Stefano de Pretis et al.   BIOINFORMATICS

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

(2015) Kathleen M. Fisch et al.   BIOINFORMATICS

The MI bundle: enabling network and structural biology in genome visualization tools: Fig. 1.

(2015) Arnaud Céol et al.   BIOINFORMATICS

GenoMetric Query Language: a novel approach to large-scale genomic data management

(2015) Marco Masseroli et al.   BIOINFORMATICS

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data

(2015) Kamal Kishore et al.   BMC BIOINFORMATICS

QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation

(2015) Prerana Wagle et al.   BMC GENOMICS

Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective

(2015) Alicia Poplawski et al.   BRIEFINGS IN BIOINFORMATICS

Multi-omic data analysis using Galaxy

(2015) Jorrit Boekel et al.   NATURE BIOTECHNOLOGY

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud

(2015) Enis Afgan et al.   PLoS One

MendeLIMS: a web-based laboratory information management system for clinical genome sequencing

(2014) Susan M Grimes et al.   BMC BIOINFORMATICS

SMITH: a LIMS for handling next-generation sequencing workflows

(2014) Francesco Venco et al.   BMC BIOINFORMATICS

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Galaxy LIMS for next-generation sequencing

(2013) J. Scholtalbers et al.   BIOINFORMATICS

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

(2013) Katherine Wolstencroft et al.   NUCLEIC ACIDS RESEARCH

The Wasp System: An open source environment for managing and analyzing genomic data

(2012) Andrew S. McLellan et al.   GENOMICS

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Galaxy CloudMan: delivering cloud compute clusters

(2011) Enis Afgan et al.   BMC BIOINFORMATICS

Chipster: user-friendly analysis software for microarray and other high-throughput data

(2011) M Aleksi Kallio et al.   BMC GENOMICS

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

SLIMS--a user-friendly sample operations and inventory management system for genotyping labs

(2010) T. Van Rossum et al.   BIOINFORMATICS

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS