PSCBS protocols

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PSCBS specifications

Information


Unique identifier OMICS_05545
Name PSCBS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.64.0
Stability Stable
Requirements
parallel, utils, R(≥3.2.0), R.methodsS3(≥1.7.1), R.oo(≥1.21.0), R.utils(≥2.5.0), R.cache(≥0.12.0), matrixStats(≥0.52.2), aroma.light(≥2.4.0), DNAcopy(≥1.42.0), listenv(≥0.6.0), future(≥1.5.0), Hmisc(≥3.16-0), R.rsp(≥0.41.0), R.devices(≥2.15.1), ggplot2(≥2.2.1)
Maintained Yes

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Maintainer


  • person_outline Henrik Bengtsson <>

Publication for PSCBS

PSCBS in pipeline

2014
PMCID: 4220069
PMID: 25270265
DOI: 10.1186/s13059-014-0470-7

[…] henrik bengtsson at university of california, san fransisco, usa and pierre neuvial, cnrs, france for useful discussions on baf bias, and henrik also for advice on using the aroma.affymetrix and pscbs r packages. we also like to acknowledge marcus mayrhofer at uppsala university, sweden for introducing us to two-dimensional patterns in snp array data in the form of taps plots. this project […]


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PSCBS in publications

 (13)
PMCID: 5923255
PMID: 29703982
DOI: 10.1038/s41467-018-04001-5

[…] the contribution of each homologous chromosome was assessed via reference and alternate read counts at the germline heterozygous sites. finally, we segmented the allele specific copy ratios using pscbs. resulting copy ratios and the force called ssnvs and indels were used as input for absolute,, to estimate the sample purity, ploidy, and cancer cell fraction (ccf) of scnas and ssnvs. […]

PMCID: 5762758
PMID: 29321523
DOI: 10.1038/s41467-017-02602-0

[…] to attenuate systematic variance in all sequenced specimens, including controls. finally, normalized fragment count statistics were used to estimate cna profiles. segmentation was performed with pscbs, segmentation files and windows used for cna estimation were converted to a compound segmentation file and marker files that were used as input for gistic2.0, and processing was performed […]

PMCID: 5731348
PMID: 29180611
DOI: 10.15252/msb.20177697

[…] in a control was recorded for the tumour and subsequently corrected for gc‐content and replication timing to remove coverage fluctuations caused by these biases. the genome was segmented using the pscbs package in r (van den meersche et al, ; olshen et al, ) while incorporating sv breakpoints defined by sophia. segments were clustered according to their coverage ratio and baf value using […]

PMCID: 5589900
PMID: 28883545
DOI: 10.1038/s41467-017-00639-9

[…] is closer). for tcga data, we utilized all available data (even if no methylation data was available) and estimated copy number using circular binary segmentation algorithm as implemented in pscbs., mutation status in cancer cell lines: we obtained mutational data for all cell lines from the repository cell line project release v76 (http://cancer.sanger.ac.uk/cell_lines)., exonic snps […]

PMCID: 5504807
PMID: 28702081
DOI: 10.1186/s13068-017-0860-7

[…] was pretreated in alkaline and acidic conditions aiming to prepare varied substrates presenting similar glucan contents, but different levels of residual xylan and lignin. chemical composition of pscbs and removal of cell wall components are presented in table . cellulose content of the pretreated bagasses was similar, varying from 50.5% (naoh pscb) to 56.1% (so2/steam pscb). as expected, […]


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PSCBS institution(s)
Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA

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