Rendered from
mBPCR.Rnwusingutils::SweavePackage: mBPCR 1.67.0
P.M.V. Rancoita
mBPCR: Bayesian Piecewise Constant Regression for DNA copy number estimation
It contains functions for estimating the DNA copy number profile using mBPCR with the aim of detecting regions with copy number changes.
Authors:
mBPCR_1.67.0.tar.gz
mBPCR_1.67.0.zip(r-4.7)mBPCR_1.67.0.zip(r-4.6)mBPCR_1.67.0.zip(r-4.5)
mBPCR_1.67.0.tgz(r-4.6-any)mBPCR_1.67.0.tgz(r-4.5-any)
mBPCR_1.67.0.tar.gz(r-4.7-any)mBPCR_1.67.0.tar.gz(r-4.6-any)
mBPCR_1.67.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
mBPCR/json (API)
| # Install 'mBPCR' in R: |
| install.packages('mBPCR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- jekoChr11Array250Knsp - Affymetrix GeneChip Mapping 250K NSP Array data of JEKO-1 cell line
- rec10k - Affymetrix GeneChip Mapping 10K Array data of REC-1 cell line
On BioConductor:mBPCR-1.67.0(bioc 3.24)mBPCR-1.66.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
acghsnpmicroarraycopynumbervariation
Last updated from:d6307b27bb. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 184 | ||
| linux-devel-x86_64 | OK | 397 | ||
| source / vignettes | OK | 267 | ||
| linux-release-x86_64 | OK | 387 | ||
| macos-release-arm64 | OK | 166 | ||
| macos-oldrel-arm64 | OK | 214 | ||
| windows-devel | OK | 253 | ||
| windows-release | OK | 236 | ||
| windows-oldrel | OK | 255 | ||
| wasm-release | OK | 175 |
Exports:centromerecomputeA10computeLA0VectcomputeMBPCRcomputePCRegcomputeRecursionscomputeRegrCurveestGlobParamestProfileWithMBPCRestProfileWithMBPCRforOligoSnpSetimportCNDataindexLA0logAddplotEstProfilewriteEstProfile
Dependencies:abindaffyiobackportsBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobbootbroomcachemclicliprcodetoolscpp11crayondata.tableDBIDelayedArrayDNAcopydplyrfastmapffforcatsforeachformula.toolsgdsfmtgenericsGenomicRangesglmnetglueGWASExactHWGWASToolshavenhmsIRangesiteratorsjomolatticelifecyclelme4lmtestlogistfmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmiceminqamitmlnlmenloptrnnetnumDerivoligoClassesoperator.toolsordinalpanpillarpkgconfigprettyunitsprogresspurrrquantregquantsmoothR6rbibutilsRcppRcppEigenRdpackreadrreformulasrlangrpartRSQLiteS4ArraysS4VectorssandwichSeqinfoshapeSparseArraySparseMstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttzdbucminfutf8vctrsvroomwithrXVectorzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Retrieve base positions of centromeres | centromere |
| Estimate the copy number profile | computeMBPCR |
| Estimate global parameters of copy number data | estGlobParam |
| Estimate and print the copy number profile of some chromosomes of a sample | estProfileWithMBPCR |
| Estimate and print the copy number profile of some chromosomes of samples in an oligoSnpSet object | estProfileWithMBPCRforOligoSnpSet |
| Import the copy number data | importCNData |
| Affymetrix GeneChip Mapping 250K NSP Array data of JEKO-1 cell line (chr. 11) | jekoChr11Array250Knsp |
| Overflow-safe computation of the logarithm of a sum | logAdd |
| Plot the estimated profile of copy number data | plotEstProfile |
| Affymetrix GeneChip Mapping 10K Array data of REC-1 cell line | rec10k |
| Write the estimated profile of copy number data | writeEstProfile |
