Dgeobj.utils

Author: jkta

August undefined, 2024

WebMay 20, 2024 · DGEobj.utils Package Overview Description. This package implements a set of utility functions to enable a limma/voom workflow capturing the results in DGEobj … WebThis package implements a set of utility functions to enable a limma/voom workflow capturing the results in the DGEobj data structure. Aside from implementing a well …

R: Differential Gene Expression (DGE) Analysis Utility …

WebJan 21, 2024 · However I'm getting the following warnings when the script ends: Warning messages: 1: In install.packages (update [instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘agricolae’ had non-zero exit status 2: In install.packages (update [instlib == l, "Package"], l, contriburl = contriburl, : installation of ... WebMay 8, 2014 · DGEobj.utils-package: DGEobj.utils Package Overview; extractCol: Extract a named column from a series of df or matrices; lowIntFilter: Apply low intensity filters to a DGEobj; rsqCalc: Calculate R-squared for each gene fit; runContrasts: Build contrast matrix and calculate contrast fits; runEdgeRNorm: Run edgeR normalization on DGEobj timeshare in destin fl

R: Calculate and add q-value and lFDR to dataframe

WebDescription. Takes a count matrix as input and converts to other desired units. Supported units include CPM, FPKM, FPK, and TPM. Output units can be logged and/or … WebrunContrasts {DGEobj.utils} R Documentation: Build contrast matrix and calculate contrast fits Description. Takes a DGEobj and a named list of contrasts to build. The DGEobj must contain a limma Fit object and associated designMatrix. Returns the DGEobj with contrast fit(s), contrast matrix, and topTable/topTreat dataframes added. WebDGEobj.utils: A toolkit facilitating a limma/voom workflow Differential Gene Expression analysis. This package implements a set of utility functions to enable a limma/voom … timeshare industry news

CRAN Task View: Genomics, Proteomics, Metabolomics, …

CRAN - Package DGEobj.utils

WebVersion: 1.42: Depends: R (≥ 3.3.0) Imports: evaluate (≥ 0.15), highr, methods, yaml (≥ 2.1.19), xfun (≥ 0.34), tools: Suggests: markdown (≥ 1.3), formatR ... WebMay 19, 2024 · DGEobj.utils: An Example Workflow John R. Thompson 2024-05-19. 1 Introduction and Setup. 1.1 Demonstration Dataset: Rat Liver Slice Compound … timeshare industry outlookWebFeb 24, 2024 · DGEobj DGEobj.utils dipsaus faux FielDHub GenomicState ggbraid ggsurvfit ggtext ggthemes ggtree healthyR.ts htmlTable industRial interactions InterCellar interpretCI lactater lgr limorhyde2 logger mdthemes MicrobiotaProcess mosaic mrf2d org pak precommit presser RBaseX rbenvo ... parasound zonemaster 650

"WebDGEobj.utils-package: DGEobj.utils Package Overview: extractCol: Extract a named column from a series of df or matrices: lowIntFilter: Apply low intensity filters to a DGEobj: rsqCalc: Calculate R-squared for each gene fit: runContrasts: Build contrast matrix and calculate contrast fits: runEdgeRNorm: Run edgeR normalization on DGEobj: runIHW " - Dgeobj.utils

Dgeobj.utils

WebThis package implements a set of utility functions to enable a limma/voom workflow capturing the results in the DGEobj data structure. Aside from implementing a well developed and popular workflow in DGEobj format, the run* functions in the package illustrate how to wrap the individual processing steps in a workflow in functions that … WebAug 4, 2024 · This is a complement/cohort to the 'DGEobj' package that provides a flexible container to manage and annotate Differential Gene Expression analysis results. DGEobj.utils: Differential Gene Expression (DGE) Analysis Utility Toolkit

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WebDGEobj.utils-package: DGEobj.utils Package Overview: convertCounts: Convert count matrix to CPM, FPKM, FPK, or TPM: extractCol: Extract a named column from a series of df or matrices: lowIntFilter: Apply low intensity filters to a DGEobj: rsqCalc: Calculate R-squared for each gene fit: runContrasts: Build contrast matrix and calculate contrast ... WebrunIHW {DGEobj.utils} R Documentation: Apply Independent Hypothesis Weighting (IHW) to a list of topTable dataframes Description. This is a wrapper around the independent hypothesis weighting package that takes a list of topTable data frames and applies Independent Hypothesis Weighting (IHW) to each topTable data frame in the list.

WebOct 5, 2024 · An extension to stopifnot() that makes it easy to declare the pre and post conditions that you code should satisfy, while also producing friendly error messages so ... WebMay 5, 2024 · DGEobj.utils-package DGEobj.utils Package Overview Description This package implements a set of utility functions to enable a limma/voom workﬂow capturing the results in DGEobj data structure. Aside from …

WebrunVoom {DGEobj.utils} R Documentation: Run functions in a typical voom/lmFit workflow Description. In the default workflow, this function runs voomWithQualityWeights followed by lmFit and optionally eBayes. If the contrasts of interest are already represented in the model, enable eBayes. To use contrasts.fit downstream, run eBayes after that ... WebextractCol {DGEobj.utils} R Documentation: Extract a named column from a series of df or matrices Description. Take a named list of dataframes where each dataframe has the same column names (e.g. a list of topTable dataframes), then extract the named column from each dataframe and return a matrix. The name of each dataframe is used as the ...

WebMay 20, 2024 · DGEobj.utils-package: DGEobj.utils Package Overview; extractCol: Extract a named column from a series of df or matrices; lowIntFilter: Apply low intensity filters to a DGEobj; rsqCalc: Calculate R-squared for each gene fit; runContrasts: Build contrast matrix and calculate contrast fits; runEdgeRNorm: Run edgeR normalization on DGEobj

WebDGEobj.utils-package: DGEobj.utils Package Overview; extractCol: Extract a named column from a series of df or matrices; lowIntFilter: Apply low intensity filters to a DGEobj; rsqCalc: Calculate R-squared for each gene fit; runContrasts: Build contrast matrix and calculate contrast fits; runEdgeRNorm: Run edgeR normalization on DGEobj parasound zonemaster 1250WebMay 5, 2024 · DGEobj.utils-package DGEobj.utils Package Overview Description This package implements a set of utility functions to enable a limma/voom workﬂow … parasound zrkWebFeb 10, 2024 · An implementation of interpreted string literals, inspired by Python's Literal String Interpolation and Docstrings timeshare in disney worldWebDGEobj.utils Package Overview. convertCounts. Convert count matrix to CPM, FPKM, FPK, or TPM. extractCol. Extract a named column from a series of df or matrices. … parasound zonemaster 250WebA collection of algorithms and functions to aid statistical modeling. Includes limiting dilution analysis (aka ELDA), growth curve comparisons, mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Also includes advanced generalized linear … parasound z phono preampWebMay 20, 2024 · DGEobj.utils-package: DGEobj.utils Package Overview; extractCol: Extract a named column from a series of df or matrices; lowIntFilter: Apply low intensity filters to a DGEobj; rsqCalc: Calculate R-squared for each gene fit; runContrasts: Build contrast matrix and calculate contrast fits; runEdgeRNorm: Run edgeR normalization on DGEobj parasound zm4 timeshare industry leaders