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Anduril specifications

Information


Unique identifier OMICS_03437
Name Anduril
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, MATLAB, Perl, Python, R
License Apache License version 2.0, GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Anduril

Anduril in pipelines

 (2)
2017
PMCID: 5508072
PMID: 27899802
DOI: 10.1038/leu.2016.365

[…] england biolabs, ipswich, ma, usa) and sequenced on a hiseq 2000 (illumina) at the genomics core facility, embl, heidelberg. rna-seq data analysis was performed with a custom pipeline implemented in anduril using gsnap for read alignment, htseq-count for read counting and deseq2 for differential gene expression analysis. gene set enrichment analysis was performed with gsea., associations […]

2017
PMCID: 5708109
PMID: 29187174
DOI: 10.1186/s12885-017-3815-2

[…] analysis toolkit (gatk). the achieved coverage in target regions was on average 80× (70% targeted regions with >30× coverage). all preprocessing and downstream analyses were performed within the anduril framework for scientific data analysis []. we performed point mutation calling using mutect (50). then, to account for potential artifacts induced by formalin-fixed paraffin embedded (ffpe) […]


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Anduril in publications

 (28)
PMCID: 5810006
PMID: 29433456
DOI: 10.1186/s12885-018-4021-6

[…] gatk. somatic single nucleotide variants (snvs) were detected by mutect [] with the high-confidence mode. copy number alterations were detected by adtex []. all pipelines and analyses were run using anduril [], a workflow framework for scientific data analysis. mean coverage per sample is given in (additional file : figure s2b)., copy number variations (cnvs) were determined by calculating […]

PMCID: 5833801
PMID: 29396433
DOI: 10.1038/s41389-017-0014-6

[…] samples were analyzed with the celigo cell imaging cytometer (brooks) to image the entire well surface and quantified with the celigo software., computational analysis was carried out with the anduril framework (pmid: 20822536). rna and microrna sequencing data was downloaded from the cancer genome atlas (tcga) for 752 unique breast tumors for which both measurement types were available […]

PMCID: 5725737
PMID: 28921546
DOI: 10.1002/ijc.31053

[…] other options default)., the complete rna‐seq analysis pipeline (including alignment, qc, differential gene expression analysis, and gsea) was implemented and run on the workflow management platform anduril (http://www.anduril.org). , to find chromosomal regions enriched for differentially expressed genes, we used the perl script “pge.pl” provided by de preter et al. this method implements […]

PMCID: 5398530
PMID: 28426742
DOI: 10.1371/journal.pone.0174898

[…] -i 15 -q 10 -l, and the human genome build 37 (hg19) was used as the reference. duplicate reads were removed with picard tools (http://picard.sourceforge.net)., sequence data were analyzed with the anduril workflow framework [] (). variants were called by varscan somatic (v.2.3.6) [] and mutect (v1.1.4) [] in tumor-normal pairs. the pileup files for varscan somatic were created using samtools […]

PMCID: 5508072
PMID: 27899802
DOI: 10.1038/leu.2016.365

[…] england biolabs, ipswich, ma, usa) and sequenced on a hiseq 2000 (illumina) at the genomics core facility, embl, heidelberg. rna-seq data analysis was performed with a custom pipeline implemented in anduril using gsnap for read alignment, htseq-count for read counting and deseq2 for differential gene expression analysis. gene set enrichment analysis was performed with gsea., associations […]


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Anduril institution(s)
Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland; Medical Biotechnology, VTT Technical Research Centre and University of Turku, Turku, Finland; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland; Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland
Anduril funding source(s)
This work was supported by Academy of Finland (projects: 125826, 128416 and 1121413; Center of Excellence in Translational Genome-Scale Biology), Sigrid Jusélius Foundation, Foundation for the Finnish Cancer Institute, Finnish Cancer Associations, Biocentrum Helsinki, Helsinki University Funds, Finnish Graduate School in Computational Sciences and Helsinki Biomedical Graduate School.

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