2024 Bumphunter cran

Bumphunter cran

Author: ttuj

August undefined, 2024

WebNov 8, 2024 · An object of class bumps. mat. A matrix with rows representing genomic locations and columns representing samples. design. Design matrix with rows representing samples and columns representing covariates. Regression is applied to each row of mat. chr. A character vector with the chromosomes of each location. pos. WebFeb 13, 2024 · Local regression, likelihood and density estimation methods as described in the 1999 book by Loader.

CRAN - Package locfit

WebNov 8, 2024 · bumphunter: Bumphunter; clusterMaker: Make clusters of genomic locations based on distance; dummyData: Generate dummy data for use with … WebNov 1, 2024 · 1 bumphunter example. The bumphunter package can be used for methylation analyses where you are interested in identifying differentially methylated regions. The vignette explains in greater detail the … move quick access toolbar to bottom of screen

Using bumphunter with non-human genomes

WebAug 21, 2024 · locfit: Local Regression, Likelihood and Density Estimation. Local regression, likelihood and density estimation methods as described in the 1999 book by … WebBioconductor version: Release (3.16) A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the ... WebNov 8, 2024 · annotateNearest: Annotate the results of nearest annotateTranscripts: Annotate transcripts bumphunter: Bumphunter clusterMaker: Make clusters of genomic locations based on distance dummyData: Generate dummy data for use with bumphunter functions getSegments: Segment a vector into positive, zero, and negative regions … move quickbooks data to new computer

bumphunter: Bumphunter in bumphunter: Bump Hunter

Example report using bumphunter results • regionReport

WebI'm attempting to use bumphunter:: ... (R 3.2.0) brew 1.0.6 2011-04-13 CRAN (R 3.2.0) bumphunter * 1.7.4 2015-01-15 Bioconductor checkmate 1.5.0 2014-10-19 CRAN (R 3.2.0) codetools 0.2.9 2014-08-21 CRAN (R 3.2.0) DBI * 0.3.1 2014-09-24 CRAN (R 3.2.0) devtools 1.6.1 2014-10-07 CRAN (R 3.2.0) digest 0.6.4 2013-12-03 CRAN (R 3.2.0) … WebLocal regression, likelihood and density estimation methods as described in the 1999 book by Loader. heat fabsWebdoRNG: Generic Reproducible Parallel Backend for 'foreach' Loops. Provides functions to perform reproducible parallel foreach loops, using independent random streams as … heatfab saf t vent ci plus

"WebI would start by reading the Details section of the bumphunter help file. Regarding the table, each row is a candidate DMR. value - is the average of the estimated coefficient (usually representing the difference between two groups) in the region. area - is the absolute value of the sum of the estimated coefficients in the region. " - Bumphunter cran

Bumphunter cran

WebI am using derfinder with the Canis familiaris genome; derfinder uses bumphunter::annotateNearest() to annotate its results; and bumphunter only annotates against hg19. (see derfinder: analyzeChr() breaks on chromosomes > 22) I'm willing to build an annotation object for Canis familiaris, but am not sure how to go about doing so. WebMar 9, 2024 · Make annotateTranscripts() and matchGenes() more flexible to handle other type of gene ids. · Issue #15 · rafalab/bumphunter · GitHub. Hi, As you can see at …

Did you know?

WebJan 25, 2024 · Error: Bioconductor version cannot be validated; no internet connection? Traceback: 1. BiocManager::install("bumphunter") 2. .version_validate(version) 3. … WebREADME.md. This is the developer version of the bumphunter R/Bioconductor package. Bioconductor build/check report.

WebNov 8, 2024 · annotateNearest: Annotate the results of nearest annotateTranscripts: Annotate transcripts bumphunter: Bumphunter clusterMaker: Make clusters of genomic locations based on distance dummyData: Generate dummy data for use with bumphunter functions getSegments: Segment a vector into positive, zero, and negative regions … WebBioconductor version: Release (3.3) Tools for finding bumps in genomic data. Author: Rafael A. Irizarry [cre, aut], Martin Aryee [aut], Kasper Daniel Hansen [aut], Hector Corrada Bravo [aut], Shan Andrews [ctb], Andrew E. Jaffe [ctb], Harris Jaffee [ctb], Leonardo Collado-Torres [ctb] Maintainer: Rafael A. Irizarry

WebJul 18, 2024 · Support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data. Webbumphunter_1.12.0.tar.gz: Windows Binary: bumphunter_1.12.0.zip: Mac OS X 10.9 (Mavericks) bumphunter_1.12.0.tgz: Subversion source (username/password: readonly) …

WebMar 13, 2015 · The text was updated successfully, but these errors were encountered:

http://leekgroup.github.io/regionReport/articles/bumphunterExample.html move quickbooks company file to new pcWebA "bumhunter" is somebody who takes a seat at an online heads-up cash game table and refuses to play anybody that isn't, in their opinion, a weak opponent. Let's give you an … move queen bowie heatfab saf t vent catalogWebDescription. Estimate regions for which a genomic profile deviates from its baseline value. Originally implemented to detect differentially methylated genomic regions between two … heatfab pipeWebThe hunt for bumps will be only be done for the estimate of this coefficient. cutoff. A numeric value. Values of the estimate of the genomic profile above the cutoff or below the negative of the cutoff will be used as candidate regions. It is possible to give two separate values (upper and lower bounds). heatfab saf-t vent installationWebMay 18, 2024 · Hi everyone, I am using bumphunter function from minfi package for patients (Healthy donors and treatments ) dataset to find DMRs. Where i design contrasts based on the individual patient's methylation level at different time points and After running the BumpHunter function, I get an output with genomic regions that start and end in the … move quickbooks failed unexpectedlyWebExample report using bumphunter results Leonardo Collado-Torres Lieber Institute for Brain Development, Johns Hopkins Medical CampusCenter for Computational Biology, Johns Hopkins University [email protected] ... CRAN (R 4.1.2) ## BiocParallel 1.28.1 2024-11-18 [1] Bioconductor ## BiocStyle * 2.22.0 2024-10-26 [1] Bioconductor ## … heat fab venting