Package: SCOPE 1.17.0

Rujin Wang

SCOPE: A normalization and copy number estimation method for single-cell DNA sequencing

Whole genome single-cell DNA sequencing (scDNA-seq) enables characterization of copy number profiles at the cellular level. This circumvents the averaging effects associated with bulk-tissue sequencing and has increased resolution yet decreased ambiguity in deconvolving cancer subclones and elucidating cancer evolutionary history. ScDNA-seq data is, however, sparse, noisy, and highly variable even within a homogeneous cell population, due to the biases and artifacts that are introduced during the library preparation and sequencing procedure. Here, we propose SCOPE, a normalization and copy number estimation method for scDNA-seq data. The distinguishing features of SCOPE include: (i) utilization of cell-specific Gini coefficients for quality controls and for identification of normal/diploid cells, which are further used as negative control samples in a Poisson latent factor model for normalization; (ii) modeling of GC content bias using an expectation-maximization algorithm embedded in the Poisson generalized linear models, which accounts for the different copy number states along the genome; (iii) a cross-sample iterative segmentation procedure to identify breakpoints that are shared across cells from the same genetic background.

Authors:Rujin Wang, Danyu Lin, Yuchao Jiang

SCOPE_1.17.0.tar.gz
SCOPE_1.17.0.zip(r-4.5)SCOPE_1.17.0.zip(r-4.4)SCOPE_1.17.0.zip(r-4.3)
SCOPE_1.17.0.tgz(r-4.4-any)SCOPE_1.17.0.tgz(r-4.3-any)
SCOPE_1.17.0.tar.gz(r-4.5-noble)SCOPE_1.17.0.tar.gz(r-4.4-noble)
SCOPE_1.17.0.tgz(r-4.4-emscripten)SCOPE_1.17.0.tgz(r-4.3-emscripten)
SCOPE.pdf |SCOPE.html✨
SCOPE/json (API)
NEWS

# Install 'SCOPE' in R:
install.packages('SCOPE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • QCmetric.scopeDemo - Pre-stored QCmetric data for demonstration purposes
  • Y_sim - A read count matrix in the toy dataset
  • coverageObj.scopeDemo - Pre-stored coverageObj.scope data for demonstration purposes
  • iCN_sim - A post cross-sample segmentation integer copy number matrix returned by SCOPE in the demo
  • normObj.scopeDemo - Pre-stored normObj.scope data for demonstration purposes
  • ref.scopeDemo - Pre-stored 500kb-size reference genome for demonstration purposes
  • ref_sim - A reference genome in the toy dataset

On BioConductor:SCOPE-1.17.0(bioc 3.20)SCOPE-1.16.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

16 exports 0.71 score 93 dependencies 56 mentions

Last updated 2 months agofrom:9989494462

Exports:get_bam_bedget_coverage_scDNAget_gcget_giniget_mappget_samp_QCinitialize_ploidyinitialize_ploidy_groupnormalize_codex2_ns_noKnormalize_scopenormalize_scope_foreachnormalize_scope_groupperform_qcplot_EM_fitplot_iCNsegment_CBScs

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsbootBSgenomeBSgenome.Hsapiens.UCSC.hg19caToolscellrangerclassclicodetoolscpp11crayoncurldata.tableDelayedArrayDescToolsDNAcopydoParallele1071ExactexpmfansiforeachformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgldgluegplotsgtoolshmshttrIRangesiteratorsjsonliteKernSmoothlambda.rlatticelifecyclelmommagrittrMASSMatrixMatrixGenericsmatrixStatsmimemvtnormopensslpillarpkgconfigprettyunitsprogressproxyR6RColorBrewerRcppRCurlreadxlrematchrestfulrRhtslibrjsonrlangrootSolveRsamtoolsrstudioapirtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrswithrXMLXVectoryamlzlibbioc

SCOPE: Single-cell Copy Number Estimation

Rujin Wang, Danyu Lin, Yuchao Jiang

Rendered fromSCOPE_vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2021-07-14
Started: 2019-09-09

Readme and manuals

Help Manual

Help pageTopics
Pre-stored coverageObj.scope data for demonstration purposescoverageObj.scopeDemo
Get bam file directories, sample names, and whole genomic binsget_bam_bed
Get read coverage from single-cell DNA sequencingget_coverage_scDNA
Compute GC contentget_gc
Compute Gini coefficients for single cellsget_gini
Compute mappabilityget_mapp
Get QC metrics for single cellsget_samp_QC
A post cross-sample segmentation integer copy number matrix returned by SCOPE in the demoiCN_sim
Ploidy pre-initializationinitialize_ploidy
Group-wise ploidy pre-initializationinitialize_ploidy_group
Normalization of read depth without latent factors under the case-control settingnormalize_codex2_ns_noK
Normalization of read depth with latent factors using Expectation-Maximization algorithm under the case-control settingnormalize_scope
Normalization of read depth with latent factors using Expectation-Maximization algorithm under the case-control setting in parallelnormalize_scope_foreach
Group-wise normalization of read depth with latent factors using Expectation-Maximization algorithm and shared clonal membershipsnormalize_scope_group
Pre-stored normObj.scope data for demonstration purposesnormObj.scopeDemo
Quality control for cells and binsperform_qc
Visualize EM fitting for each cell.plot_EM_fit
Plot post-segmentation copy number profiles of integer valuesplot_iCN
Pre-stored QCmetric data for demonstration purposesQCmetric.scopeDemo
A reference genome in the toy datasetref_sim
Pre-stored 500kb-size reference genome for demonstration purposesref.scopeDemo
Cross-sample segmentationsegment_CBScs
A read count matrix in the toy datasetY_sim