Dgeobj.utils

Author: qswn

August undefined, 2024

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. 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.

CRAN - Package knitr

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 Overview. convertCounts. Convert count matrix to CPM, FPKM, FPK, or TPM. extractCol. Extract a named column from a series of df or matrices. … maverick digital candy thermometer

CRAN - Package DGEobj.utils

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 5, 2024 · DGEobj.utils-package DGEobj.utils Package Overview Description This package implements a set of utility functions to enable a limma/voom workﬂow … WebMay 19, 2024 · DGEobj.utils: Differential Gene Expression (DGE) Analysis Utility Toolkit. Provides a function toolkit to facilitate reproducible RNA-Seq Differential Gene … herman mailly

Dgeobj.utils

R: Build contrast matrix and calculate contrast fits

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 ... 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

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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 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 ...

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 ... 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

WebFeb 10, 2024 · An implementation of interpreted string literals, inspired by Python's Literal String Interpolation and Docstrings 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).

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 …

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 ... herman manufacturing llcWebApr 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 … herman lyngeWebThis 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 … herman manufacturing companyWebMar 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, … maverick digital thermometer instructionsWebThis 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 … maverick digital remote thermometerWebMay 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 maverick digital shopWebrunContrasts {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. maverick digital hood / grill lid thermometer