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PSCBS specifications


Unique identifier OMICS_05545
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
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




No version available



  • person_outline Henrik Bengtsson

Publication for PSCBS

PSCBS citations


Whole exome sequencing of cell free DNA and circulating tumor cells in multiple myeloma

Nat Commun
PMCID: 5923255
PMID: 29703982
DOI: 10.1038/s41467-018-04001-5

[…] en, 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. ABOSOLUTE […]


Integrative genomic and transcriptomic analysis of leiomyosarcoma

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

[…] used 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 with d […]


Screening drug effects in patient‐derived cancer cells links organoid responses to genome alterations

Mol Syst Biol
PMCID: 5731348
PMID: 29180611
DOI: 10.15252/msb.20177697

[…] ty 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 k‐mean […]


Copy number rather than epigenetic alterations are the major dictator of imprinted methylation in tumors

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

[…] hichever 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 ( […]


Limitation of cellulose accessibility and unproductive binding of cellulases by pretreated sugarcane bagasse lignin

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

[…] CB) 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, cell […]


Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus

Plant Biotechnol J
PMCID: 5633767
PMID: 28370938
DOI: 10.1111/pbi.12732

[…] ocks was calculated using an R script, and adjacent blocks with the same coverage value were aggregated to consecutive segments using a circular binary segmentation algorithm implemented in R package PSCBS (Bengtsson et al., ; Olshen et al., ). Adjacent segments over 50 kb in length and with the same mean coverage value were merged unless separated by gaps larger than 50 kb.Mean read coverage and […]


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

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