2024 Dgeobj.utils

Dgeobj.utils

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August undefined, 2024

WebDGEobj.utils: Differential Gene Expression (DGE) Analysis Utility Toolkit. Provides a function toolkit to facilitate reproducible RNA-Seq Differential Gene Expression (DGE) analysis …

DGEobj.utils A Limma/voom workflow capturing output in …

WebDGEobj.utils — Differential Gene Expression (DGE) Analysis Utility Toolkit - DGEobj.utils/MD5 at master · cran/DGEobj.utils :exclamation: This is a read-only mirror of the CRAN R package repository. 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 chips like cheetos

DGEobj.utils: Differential Gene Expression (DGE) Analysis Utility ...

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 … WebMar 28, 2024 · The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows by m-samples dimensions) and metadata (not keyed to row, col, or assays). A set … 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 … chip slim driver

DGEobj.utils: An Example Workflow - cran.r-project.org

R: Build contrast matrix and calculate contrast fits

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. WebApr 3, 2024 · After differential analysis, DGEobj and DGEobj.utils provide a flexible container and a function toolkit to manage and annotate Differential Gene Expression (DGE) analysis results. Clustering: HTSCluster contains a model based on Poisson mixture to cluster RNA-seq datasets. Misc: SIBERG implements a method to identify bimodally … chips lilasWebMar 28, 2024 · The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows by m-samples dimensions) and metadata (not keyed to row, col, or assays). A set of accessory functions to deposit, query and retrieve subsets of a data workflow has been provided. Attributes are used to capture metadata such as species and gene model, … chips like ruffles

"WebDetails. The qvalue package from John Storey at Princeton takes a list of p-values and calculates a q-value and a Local FDR (lFDR). The q-value is essentially a less conservative FDR estimate compared to the default Benjamini-Hochberg FDR produced by topTable analysis (i.e. will give more differential genes at the same nominal cutoff). " - Dgeobj.utils

Dgeobj.utils

CRAN Task View: Genomics, Proteomics, Metabolomics, …

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 …

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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 … 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: Differential Gene Expression (DGE) Analysis Utility Toolkit. Provides a function toolkit to facilitate reproducible RNA-Seq Differential Gene … WebA 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 …

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 … Run a workflow on any GitHub event. Kick off workflows with GitHub events like … Secure platform, secure data We’re constantly improving our security, audit, … Project planning for developers. Create issues, break them into tasks, track … Learn about GitHub Discussions, a collaboration tool & forum connecting … 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 Package Overview. convertCounts. Convert count matrix to CPM, FPKM, FPK, or TPM. extractCol. Extract a named column from a series of df or matrices. …

WebFeb 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 ... graphene nanoribbon spin-photodetectorWebDescription. 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 … graphene new materialWebFeb 10, 2024 · An implementation of interpreted string literals, inspired by Python's Literal String Interpolation and Docstrings graphene nitrideWebDGEobj.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 chip slimdriversWebextractCol {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 ... chips line artWebMay 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 chips lindsayWebAug 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 graphene nyse