Galaxy statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Galaxy
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Tool usage distribution map

This map represents all the scientific publications referring to Galaxy per scientific context
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Associated diseases

This word cloud represents Galaxy usage per disease context
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Popular tool citations

chevron_left Read quality control SNP detection SNV detection Alignment evaluation Known transcript quantification File format conversion Workflow management systems Differential expression Sequence alignment visualization Network visualization De novo transcriptome assembly Duplicate read removal Structural motif detection File filtering Indel detection Peak calling Tag count Variant detection Variant detection Depth of coverage File intersection File sorting chevron_right
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Protocols

Galaxy specifications

Information


Unique identifier OMICS_01141
Name Galaxy
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • FASTQ Groomer

Maintainer


  • person_outline Daniel Blankenberg

Publications for Galaxy

Galaxy citations

 (903)
library_books

Copy number variants implicate cardiac function and development pathways in earthquake induced stress cardiomyopathy

2018
Sci Rep
PMCID: 5954162
PMID: 29765130
DOI: 10.1038/s41598-018-25827-5

[…] tential variant locus. Variants were annotated and analysed using Ingenuity Variant Analysis (IVA) software (QIAGEN, Redwood City, CA, USA), MutationTaster2, SnpEff, SeattleSeq annotation server, and Galaxy (via usegalaxy.org). Allele frequencies and additional annotations were drawn from 1000 Genomes project, NHLBI GO Exome Sequencing Project (ESP), Seattle, WA (http://evs.gs.washington.edu/EVS/) […]

library_books

Effect of Bmi1 over expression on gene expression in adult and embryonic murine neural stem cells

2018
Sci Rep
PMCID: 5945652
PMID: 29749381
DOI: 10.1038/s41598-018-25921-8

[…] accompanying p-values (paired t-test) and false discovery rates. For RNA-seq, reads were aligned to the genome (mm9 genome build) and transcripts assigned using Tophat, Cufflinks, and Cuffdiff at the Galaxy server,. Further analysis was performed using Excel. Clustering was performed using Cluster 3.0 (http://bonsai.ims.utokyo.ac.jp/Bmdehoon/software/cluster/) and visualized using Java Treeview (h […]

library_books

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

2018
Front Microbiol
PMCID: 5945981
PMID: 29780368
DOI: 10.3389/fmicb.2018.00836

[…] s in S. Enteritidis genomes from known outbreaks (n = 111) were extracted from PHASTER results and aligned with Multiple Alignment using Fast Fourier Transform (MAFFT; Katoh and Standley, ) tool from Galaxy platform (https://usegalaxy.org) and the alignment tree file was uploaded to iTOL platform for editing. We conducted an analysis of similarity (ANOSIM) on the prophage sequence profiles using Q […]

library_books

Correlation Analyses Reveal a Limited Role of Transcription in Genome Wide Differential MicroRNA Expression in Mammals

2018
Front Genet
PMCID: 5946028
PMID: 29780403
DOI: 10.3389/fgene.2018.00154

[…] above from both the 5′ and 3′ ends of the pri-miRNAs, and then search for overlaps with Pol2 ChIP-seq data. Notably, the median length of human pri-miRNAs is approximately 41 kb, mouse 36 kb (). The Galaxy website was used to find overlaps and join different datasets into single files for correlation studies (). For ChIP-seq, we considered Pol2 peaks on both DNA strands. For RNA-seq, we considere […]

library_books

Transcriptome reprogramming of resistant and susceptible peach genotypes during Xanthomonas arboricola pv. pruni early leaf infection

2018
PLoS One
PMCID: 5919700
PMID: 29698473
DOI: 10.1371/journal.pone.0196590

[…] e for gene models fully compatible with the format accepted by the first script, a reads mapping session was performed using TopHat followed by the Cufflinks and Cuffmerge tools (Table B in ), on the Galaxy open source web-based platform []. Cuffmerge output GTF file and TopHat output BAM alignment files were exported and used as input for the first and the second Python scripts, respectively. Sub […]

call_split

EZH2 inhibitors sensitize myeloma cell lines to panobinostat resulting in unique combinatorial transcriptomic changes

2018
Oncotarget
PMCID: 5955152
PMID: 29774113
DOI: 10.18632/oncotarget.25128
call_split See protocol

[…] analysis (FastQC), processed (FASTQ and Tophat2(aligned to hg19)), analyzed for differential expression (Cufflinks and Cuffdiff) and visualized (CummeRbund) using the open source, web-based platform Galaxy []. Downstream subsetting and analysis was conducted using the R programing language and Ingenuity Pathway Analysis (IPA; QIAGEN; Venlo, Netherlands). Differential expression was considered sig […]


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Galaxy institution(s)
Department of Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Albert-Ludwigs-University, Freiburg, Freiburg, Germany; Institut Curie, PSL Research University, Paris, France; Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA; Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany; Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Biomedical Engineering, Oregon Health and Science University, OR, USA; Earlham Institute, Norwich Research Park, Norwich, UK; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
Galaxy funding source(s)
Supported by the National Human Genome Research Institute, National Institutes of Health [HG006620, HG005133, HG004909 and HG005542]; NSF [DBI 0543285, 0850103 and 1661497]; Huck Institutes for the Life Sciences at Penn State; and, in part, under a grant with the Pennsylvania Department of Health using Tobacco Settlement Funds.

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