AneuFinder protocols

View AneuFinder computational protocol

AneuFinder statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Aneuploidy analysis CNV annotation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

AneuFinder specifications

Information


Unique identifier OMICS_15772
Name AneuFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.8.0
Stability Stable
Requirements
methods, stats, graphics, IRanges, GenomicRanges, Rsamtools, DNAcopy, utils, testthat, S4Vectors, GenomeInfoDb, Biostrings, BiocStyle, grDevices, GenomicAlignments, ggplot2, ggrepel, BSgenome.Hsapiens.UCSC.hg19, R(>=3.3), knitr, reshape2, foreach, BSgenome.Mmusculus.UCSC.mm10, mclust, doParallel, cowplot, ggdendro, bamsignals, AneuFinderData, ecp, ReorderCluster
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Floris Foijer <>

Publication for AneuFinder

AneuFinder in pipeline

2016
PMCID: 4888403
PMID: 27246599
DOI: 10.1186/s13059-016-0976-2

[…] bam files were sorted using samtools (version 0.1.18) [] and duplicate reads were marked using bamutil (version 1.0.3). duplicate reads and ambiguous alignments (mapq >10) were filtered out using aneufinder. estimated complexity was calculated by downsampling the reads several times and determining the fraction of unique reads each time. then the number of reads sequenced (seq_reads) […]


To access a full list of citations, you will need to upgrade to our premium service.

AneuFinder in publications

 (3)
PMCID: 5773480
PMID: 29348659
DOI: 10.1038/s41467-017-02760-1

[…] fpkm values were calculated for all genes and based on these genes were assigned active (fpkm > 1) or silent (fpkm < 1) status., aligned libraries were analyzed as previously described using aneufinder r package using the following settings: low-quality alignments (mapping quality score (mapq) < 10) and duplicate reads were excluded and read counts in 2 mb variable-width bins […]

PMCID: 5400506
PMID: 28318489
DOI: 10.7554/eLife.20873.028

[…] previously () in an automated fashion (agilent bravo robot). single cell libraries were pooled an analyzed on an illumina hiseq2500 sequencer. single cell sequencing data was analyzed using aneufinder software as described previously ()., rna was isolated using the rneasy kit (qiagen). for qpcr reactions, 1 µg of total rna was used for a reverse transcriptase reaction (superscript ii, […]

PMCID: 4888403
PMID: 27246599
DOI: 10.1186/s13059-016-0976-2

[…] the reference genome is rather even which allows accurate calls of chromosome copy number.fig. 1, the copy number state of each chromosome was determined using an in-house developed algorithm called aneufinder []. briefly, this algorithm bins the mapped reads and uses a hidden markov model (hmm) to predict the copy number state (i.e. monosomic, disomic, trisomic, etc.) for each bin. […]


To access a full list of publications, you will need to upgrade to our premium service.

AneuFinder funding source(s)
This work was supported by a Dutch Cancer Society grant (KWF grant RUG-2012-5549) and a Groningen Foundation for Paediatric Oncology (SKOG) grant, and by an NWO (The Netherlands Organisation for Scientific Research) MEERVOUD grant and a University of Groningen Rosalind Franklin Fellowship grant.

AneuFinder reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review AneuFinder