Dgeobj.utils

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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 … 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 …

R: Convert count matrix to CPM, FPKM, FPK, or TPM

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. … 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 ... ralf rangnick interview man utd

DGEobj.utils/MD5 at master · cran/DGEobj.utils · GitHub

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 … 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. overacting quotes

R error: installation of package had non-zero exit status

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

"WebDGE.Tools2: RNA-Seq Analysis Workflow Package (deprecated: See DGEobj, DGEobj.utils and DGEobj.plots) DGE.Tools2 is a suite of functions to facilitate and standardize RNA-Seq DGE analysis. DGE.Tools relies on the DGEobj data structure to store DGE data and analysis results. " - Dgeobj.utils

Dgeobj.utils

R: Differential Gene Expression (DGE) Analysis Utility Toolkit

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 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).

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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 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 …

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 19, 2024 · DGEobj.utils: Differential Gene Expression (DGE) Analysis Utility Toolkit. Provides a function toolkit to facilitate reproducible RNA-Seq Differential Gene …

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 ... 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

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

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 … ralf rangnick newcastleWebVersion: 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 ... over actionWebThis 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 … ralf rankWebThis 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 … overacting stand upWebFeb 10, 2024 · An implementation of interpreted string literals, inspired by Python's Literal String Interpolation and Docstrings ralf rangnick new 2021WebDGEobj.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 ... ralf rangnick managerial recordWebextractCol {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 ... ralf rangnick photos