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Protocols

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

Versioning


No version available

Publication for Anduril

Anduril citations

 (19)
library_books

Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis enriched mutations in the A kinase anchoring protein family (AKAPs)

2018
BMC Cancer
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). […]

library_books

Let 7 microRNA controls invasion promoting lysosomal changes via the oncogenic transcription factor myeloid zinc finger 1

2018
Oncogenesis
PMCID: 5833801
PMID: 29396433
DOI: 10.1038/s41389-017-0014-6

[…] 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 (PM […]

call_split

Intra tumor heterogeneity in breast cancer has limited impact on transcriptomic based molecular profiling

2017
BMC Cancer
PMCID: 5708109
PMID: 29187174
DOI: 10.1186/s12885-017-3815-2
call_split See protocol

[…] nome 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) sa […]

call_split

Neuroblastoma cells undergo transcriptomic alterations upon dissemination into the bone marrow and subsequent tumor progression

2017
Int J Cancer
PMCID: 5725737
PMID: 28921546
DOI: 10.1002/ijc.31053
call_split See protocol

[…] ll 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). […]

library_books

Multiple components of PKA and TGF β pathways are mutated in pseudomyxoma peritonei

2017
PLoS One
PMCID: 5398530
PMID: 28426742
DOI: 10.1371/journal.pone.0174898

[…] 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 mp […]

call_split

Genomic and transcriptional landscape of P2RY8 CRLF2 positive childhood acute lymphoblastic leukemia

2017
Leukemia
PMCID: 5508072
PMID: 27899802
DOI: 10.1038/leu.2016.365
call_split See protocol

[…] 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. […]

Citations

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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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