Package: BUScorrect 1.23.0

Xiangyu Luo

BUScorrect: Batch Effects Correction with Unknown Subtypes

High-throughput experimental data are accumulating exponentially in public databases. However, mining valid scientific discoveries from these abundant resources is hampered by technical artifacts and inherent biological heterogeneity. The former are usually termed "batch effects," and the latter is often modelled by "subtypes." The R package BUScorrect fits a Bayesian hierarchical model, the Batch-effects-correction-with-Unknown-Subtypes model (BUS), to correct batch effects in the presence of unknown subtypes. BUS is capable of (a) correcting batch effects explicitly, (b) grouping samples that share similar characteristics into subtypes, (c) identifying features that distinguish subtypes, and (d) enjoying a linear-order computation complexity.

Authors:Xiangyu Luo <[email protected]>, Yingying Wei <[email protected]>

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BUScorrect/json (API)
NEWS

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

Peer review:

Datasets:

On BioConductor:BUScorrect-1.23.0(bioc 3.20)BUScorrect-1.22.0(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 0.61 score 33 dependencies

Last updated 2 months agofrom:c3ba6b2c41

Exports:adjusted_valuesbaseline_expression_valuesBIC_BUSBUSgibbscalculate_EPSR_gammacalculate_EPSR_mucalculate_EPSR_sigma_sqestimate_IG_indicatorsIG_indexlocation_batch_effectspostprob_DEpostprob_DE_thr_funscale_batch_effectssubtype_effectsSubtypesvisualize_data

Dependencies:abindaskpassBiobaseBiocGenericsbitopscaToolscrayoncurlDelayedArrayGenomeInfoDbGenomeInfoDbDataGenomicRangesgplotsgtoolshttrIRangesjsonliteKernSmoothlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

BUScorrect_user_guide

Rendered fromBUScorrect_user_guide.Rnwusingknitr::knitron Jun 30 2024.

Last update: 2018-07-23
Started: 2018-06-26

Readme and manuals

Help Manual

Help pageTopics
Batch Effects Correction with Unknown SubtypesBUScorrect-package BUScorrect
Obtain adjusted expression values from the output by BUSgibbsadjusted_values
Obtain the baseline expression values from the output by BUSgibbsbaseline_expression_values
Obtain BIC form the output by BUSgibbsBIC_BUS
A simulated data setBUSexample_data
Batch Effects Correction and Subtype Discovery using Gibbs SamplerBUSgibbs
Calculate the estimated potential scale reduction factors (EPSR factors) for location batch effectscalculate_EPSR_gamma
Calculate the estimated potential scale reduction factors (EPSR factors) for subtype effectscalculate_EPSR_mu
Calculate the estimated potential scale reduction factors (EPSR factors) for the variances of expression valuescalculate_EPSR_sigma_sq
Estimate the intrinsic gene indicatorsestimate_IG_indicators
Obtain the intrinsic gene indicesIG_index
Obtain the location batch effects from the output by BUSgibbslocation_batch_effects
Calculate the posterior probability of being differentially expressedpostprob_DE
Select the the posterior probability threshold to control the false discovery ratepostprob_DE_thr_fun
Print the output by BUSgibbsprint.BUSfits
Obtain the scale batch effects from the output by 'BUSgibbs'scale_batch_effects
Obtain the subtype effects from the output by 'BUSgibbs'subtype_effects
Obtain the subtype indicators from the output by 'BUSgibbs'Subtypes
Summary the output by 'BUSgibbs'summary.BUSfits
Visualize the gene expression data from multiple batchesvisualize_data