Tag: RUnit

Bioconductor – genomation

DOI: 10.18129/B9.bioc.genomation     Summary, annotation and visualization of genomic data Bioconductor version: Release (3.6) A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome…

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Bioconductor – hu35ksubd.db

DOI: 10.18129/B9.bioc.hu35ksubd.db     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see hu35ksubd.db. Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubd) Bioconductor version: 3.12 Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubd) assembled using data from public repositories Author: Marc Carlson…

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Bioconductor – hgug4112a.db

DOI: 10.18129/B9.bioc.hgug4112a.db   Agilent “Human Genome, Whole” annotation data (chip hgug4112a) Bioconductor version: Release (3.18) Agilent “Human Genome, Whole” annotation data (chip hgug4112a) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“hgug4112a.db”)): Installation To install this package,…

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Bioconductor – RTN

DOI: 10.18129/B9.bioc.RTN     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RTN. RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons Bioconductor version: 3.12 A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target…

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Bioconductor – hgu95av2.db

DOI: 10.18129/B9.bioc.hgu95av2.db   Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) Bioconductor version: Release (3.18) Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“hgu95av2.db”)): Installation To install this package,…

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Bioconductor – IFAA (development version)

DOI: 10.18129/B9.bioc.IFAA   This is the development version of IFAA; for the stable release version, see IFAA. Robust Inference for Absolute Abundance in Microbiome Analysis Bioconductor version: Development (3.19) This package offers a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome…

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Bioconductor – hu35ksubc.db

DOI: 10.18129/B9.bioc.hu35ksubc.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see hu35ksubc.db. Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubc) Bioconductor version: 3.11 Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubc) assembled using data from public repositories Author: Marc Carlson…

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Bioconductor – hugene11sttranscriptcluster.db

DOI: 10.18129/B9.bioc.hugene11sttranscriptcluster.db     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see hugene11sttranscriptcluster.db. Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster) Bioconductor version: 3.10 Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster) assembled using data from public repositories Author: James W. MacDonald Maintainer: Biocore Package Maintainer <maintainer…

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Bioconductor – gDNAx

DOI: 10.18129/B9.bioc.gDNAx   Diagnostics for assessing genomic DNA contamination in RNA-seq data Bioconductor version: Release (3.18) Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and,…

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Bioconductor – dreamlet

DOI: 10.18129/B9.bioc.dreamlet   Cohort-scale differential expression analysis of single cell data using linear (mixed) models Bioconductor version: Release (3.18) Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of…

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Bioconductor – Category

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see Category. Category Analysis Bioconductor version: 2.14 A collection of tools for performing category analysis. Author: R. Gentleman with contributions from S. Falcon and D.Sarkar Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from…

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Bioconductor – AnnotationHub

DOI: 10.18129/B9.bioc.AnnotationHub     Client to access AnnotationHub resources Bioconductor version: Release (3.6) This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be…

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Import a Bioconductor package that is only used in a vignette/.Rmd script

My Bioconductor package is receiving Errors about a package not existing. I have an R package with Bioconductor. In the vignettes folder, I have several .Rmd files that have the following chunk at the top: title: ‘Manuscripts’ package: pkgName bibliography: pkgName.bib output: **BiocStyle**::html_document: toc_float: true tidy: TRUE border-width: 5px vignette:…

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Bioconductor – CDI

DOI: 10.18129/B9.bioc.CDI   Clustering Deviation Index (CDI) Bioconductor version: Release (3.18) Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be…

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Bioconductor – MmAgilentDesign026655.db

DOI: 10.18129/B9.bioc.MmAgilentDesign026655.db   Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655) Bioconductor version: Release (3.18) Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within…

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Bioconductor – hgug4101a.db

DOI: 10.18129/B9.bioc.hgug4101a.db   Agilent Human 2 cDNA Microarry Kit annotation data (chip hgug4101a) Bioconductor version: Release (3.18) Agilent Human 2 cDNA Microarry Kit annotation data (chip hgug4101a) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“hgug4101a.db”)): Installation…

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How to install or uninstall “r-bioc-genomeinfodb” on Linux Mint 21 “Vanessa” ?

1. Install r-bioc-genomeinfodb package In this section, we are going to explain the necessary steps to install r-bioc-genomeinfodb package: sudo apt install r-bioc-genomeinfodb Copy 2. Uninstall / Remove r-bioc-genomeinfodb package Please follow the guidance below to uninstall r-bioc-genomeinfodb package: sudo apt remove r-bioc-genomeinfodb Copy sudo apt autoclean && sudo apt…

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Bioconductor – DelayedArray

DOI: 10.18129/B9.bioc.DelayedArray     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see DelayedArray. A unified framework for working transparently with on-disk and in-memory array-like datasets Bioconductor version: 3.11 Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to…

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Bioconductor – GreyListChIP

DOI: 10.18129/B9.bioc.GreyListChIP     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see GreyListChIP. Grey Lists — Mask Artefact Regions Based on ChIP Inputs Bioconductor version: 3.11 Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during…

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Bioconductor – hugene21sttranscriptcluster.db

DOI: 10.18129/B9.bioc.hugene21sttranscriptcluster.db     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see hugene21sttranscriptcluster.db. Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) Bioconductor version: 3.10 Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) assembled using data from public repositories Author: James W. MacDonald Maintainer: Biocore Package Maintainer <maintainer…

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Bioconductor – fgga

DOI: 10.18129/B9.bioc.fgga   Hierarchical ensemble method based on factor graph Bioconductor version: Release (3.17) Package that implements the FGGA algorithm. This package provides a hierarchical ensemble method based ob factor graphs for the consistent cross-ontology annotation of protein coding genes. FGGA embodies elements of predicate logic, communication theory, supervised learning…

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Bioconductor – hgug4111a.db

DOI: 10.18129/B9.bioc.hgug4111a.db     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see hgug4111a.db. Agilent Human 1B annotation data (chip hgug4111a) Bioconductor version: 3.12 Agilent Human 1B annotation data (chip hgug4111a) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer…

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Bioconductor – hgu133a2.db

DOI: 10.18129/B9.bioc.hgu133a2.db     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see hgu133a2.db. Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2) Bioconductor version: 3.13 Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor…

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Bioconductor – zenith

DOI: 10.18129/B9.bioc.zenith   Gene set analysis following differential expression using linear (mixed) modeling with dream Bioconductor version: Release (3.17) Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method…

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Bioconductor – SCArray.sat

DOI: 10.18129/B9.bioc.SCArray.sat   Large-scale single-cell RNA-seq data analysis using GDS files and Seurat Bioconductor version: Release (3.17) Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to…

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Bioconductor – mpra

DOI: 10.18129/B9.bioc.mpra     Analyze massively parallel reporter assays Bioconductor version: Release (3.14) Tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA). Author: Leslie Myint [cre, aut], Kasper D. Hansen [aut] Maintainer: Leslie Myint <leslie.myint at gmail.com> Citation (from within R, enter citation(“mpra”)): Installation…

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Bioconductor – moex10sttranscriptcluster.db

DOI: 10.18129/B9.bioc.moex10sttranscriptcluster.db     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see moex10sttranscriptcluster.db. Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) Bioconductor version: 3.15 Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) assembled using data from public repositories Author: James W. MacDonald Maintainer: Biocore Package Maintainer <maintainer…

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Bioconductor – ragene21stprobeset.db

DOI: 10.18129/B9.bioc.ragene21stprobeset.db     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see ragene21stprobeset.db. Affymetrix ragene21 annotation data (chip ragene21stprobeset) Bioconductor version: 3.15 Affymetrix ragene21 annotation data (chip ragene21stprobeset) assembled using data from public repositories Author: James W. MacDonald Maintainer: Biocore Package Maintainer <maintainer…

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Bioconductor – hgu95a.db

DOI: 10.18129/B9.bioc.hgu95a.db     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see hgu95a.db. Affymetrix Human Genome U95 Set annotation data (chip hgu95a) Bioconductor version: 3.12 Affymetrix Human Genome U95 Set annotation data (chip hgu95a) assembled using data from public repositories Author: Marc Carlson…

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Bioconductor – ISLET

DOI: 10.18129/B9.bioc.ISLET   Individual-Specific ceLl typE referencing Tool Bioconductor version: Release (3.17) ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture…

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Bioconductor – shinyMethyl

DOI: 10.18129/B9.bioc.shinyMethyl     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see shinyMethyl. Interactive visualization for Illumina methylation arrays Bioconductor version: 3.15 Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported. Author: Jean-Philippe Fortin [cre, aut],…

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Failing to publish/deploy a shiny app to an Posit Connect because of Bioconductor – Posit Connect

I have a shiny app the I’ve been publishing to a Posit Connect server hosted by the HPC at my institution. The app is from my RStudio on my laptop . The Cluster has configured Posit Connect to use Package Manager to host and vet packages for security and stability….

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Bioconductor – CNORfeeder

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see CNORfeeder. Integration of CellNOptR to add missing links Bioconductor version: 2.13 This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with…

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Bioconductor – MSnID

DOI: 10.18129/B9.bioc.MSnID     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MSnID. Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications Bioconductor version: 3.13 Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search…

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Bioconductor – trackViewer

DOI: 10.18129/B9.bioc.trackViewer   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see trackViewer. A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data Bioconductor version: 3.16 Visualize mapped reads along with annotation as…

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Bioconductor – BaseSpaceR

DOI: 10.18129/B9.bioc.BaseSpaceR     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see BaseSpaceR. R SDK for BaseSpace RESTful API Bioconductor version: 3.13 A rich R interface to Illumina’s BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools. Author:…

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Bioconductor – geneplast

DOI: 10.18129/B9.bioc.geneplast     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see geneplast. Evolutionary and plasticity analysis of orthologous groups Bioconductor version: 3.13 Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses…

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Bioconductor – SICtools

DOI: 10.18129/B9.bioc.SICtools     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SICtools. Find SNV/Indel differences between two bam files with near relationship Bioconductor version: 3.12 This package is to find SNV/Indel differences between two bam files with near relationship in a way…

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Bioconductor – IMAS

DOI: 10.18129/B9.bioc.IMAS     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see IMAS. Integrative analysis of Multi-omics data for Alternative Splicing Bioconductor version: 3.12 Integrative analysis of Multi-omics data for Alternative splicing. Author: Seonggyun Han, Younghee Lee Maintainer: Seonggyun Han <hangost at ssu.ac.kr>…

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Bioconductor – mgu74b.db

DOI: 10.18129/B9.bioc.mgu74b.db     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see mgu74b.db. Affymetrix Murine Genome U74v2 annotation data (chip mgu74b) Bioconductor version: 3.10 Affymetrix Murine Genome U74v2 annotation data (chip mgu74b) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor…

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Bioconductor – mgu74c.db (development version)

DOI:10.18129/B9.bioc.mgu74c.db This is thedevelopmentversion of mgu74c.db; for the stable release version, seemgu74c.db. Affymetrix Affymetrix MG_U74C Array annotation data (chip mgu74c) Bioconductor version: Development (3.17) Affymetrix Affymetrix MG_U74C Array annotation data (chip mgu74c) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer Citation (from within R, entercitation(“mgu74c.db”)):…

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Bioconductor – gdsfmt

DOI: 10.18129/B9.bioc.gdsfmt     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see gdsfmt. R Interface to CoreArray Genomic Data Structure (GDS) Files Bioconductor version: 3.15 Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms…

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Bioconductor – SeqArray

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see SeqArray. Big Data Management of Whole-genome Sequence Variant Calls Bioconductor version: 3.4 Big data management of whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls)…

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[bullseye] r-cran-ggplot2 depends on missing libpq5 v13.8

Hi, I am on bullseye and am trying to install the package r-cran-ggplot2. This fails with E: Failed to fetch deb.debian.org/debian/pool/main/p/postgresql-13/libpq5_13.8-0%2bdeb11u1_amd64.deb 404 Not Found [IP: 146.75.122.132 80] (full output below). There seems to be a dependency on libpq5 version 13.8 whereas the version available for bullseye is 13.9. Any ideas how to…

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Bioconductor – GEOquery

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see GEOquery. Get data from NCBI Gene Expression Omnibus (GEO) Bioconductor version: 2.9 The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this…

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Bioconductor – IRanges

Infrastructure for manipulating intervals on sequences Bioconductor version: 2.6 The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially, as well as views on these sequences. Efficient list-like classes are also provided…

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Bioconductor – Rgraphviz

DOI: 10.18129/B9.bioc.Rgraphviz     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Rgraphviz. Provides plotting capabilities for R graph objects Bioconductor version: 3.13 Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package. Author: Kasper…

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Bioconductor – OrganismDbi

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see OrganismDbi. Software to enable the smooth interfacing of different database packages. Bioconductor version: 2.11 The package enables a simple unified interface to several annotation packages each of which has its own schema by…

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Bioconductor – PartheenMetaData.db

DOI: 10.18129/B9.bioc.PartheenMetaData.db     PartheenMetaData swegene.onk.lu.se Annotation Data (PartheenMetaData) Bioconductor version: Release (3.14) PartheenMetaData swegene.onk.lu.se Annotation Data (PartheenMetaData) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“PartheenMetaData.db”)): Installation To install this package, start R (version “4.1”) and…

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Bioconductor – DMRcaller

DOI: 10.18129/B9.bioc.DMRcaller     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see DMRcaller. Differentially Methylated Regions caller Bioconductor version: 3.12 Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is…

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Bioconductor – metaseqR2

DOI: 10.18129/B9.bioc.metaseqR2     An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms Bioconductor version: Release (3.11) Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining…

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Gentoo Portage Overlays – sci-BIOC/S4Vectors

Foundation of vector-like and li… (see metadata) Screenshots S4Vectors-0.22.1 ~amd64 r_suggests_biocstyle r_suggests_data_table r_suggests_delayedarray r_suggests_graph r_suggests_iranges r_suggests_matrix r_suggests_runit byte-compile View      Download      Browse     License: Artistic-2    USE Flags r_suggests_biocstyle * This flag is undocumented * r_suggests_data_table * This flag is undocumented * r_suggests_delayedarray * This flag is undocumented * r_suggests_graph…

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Bioconductor – samExploreR

DOI: 10.18129/B9.bioc.samExploreR     This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see samExploreR. samExploreR…

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Bioconductor – illuminaHumanv4.db

DOI: 10.18129/B9.bioc.illuminaHumanv4.db     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see illuminaHumanv4.db. Illumina HumanHT12v4 annotation data (chip illuminaHumanv4) Bioconductor version: 3.12 Illumina HumanHT12v4 annotation data (chip illuminaHumanv4) assembled using data from public repositories Author: Mark Dunning, Andy Lynch, Matthew Eldridge Maintainer: Mark…

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Bioconductor – HPiP

DOI: 10.18129/B9.bioc.HPiP     Host-Pathogen Interaction Prediction Bioconductor version: Release (3.15) HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data…

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[BioC] rtracklayer 1.6: invalid class “ucscCart” object

Dear Bioc, Following the rtracklayer documentation, section 2.2.4, ‘A Shortcut’, I encounter the following error browseGenome (subTargetTrack) Error in validObject(.Object) :invalid class “ucscCart” object: superclass “ANYTHING” not defined in the environment of the object’s class traceback () 13: stop(msg, ” “, errors, domain = NA)12: validObject(.Object)11: initialize(value, …)10: initialize(value, …)9:…

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Bioconductor – neaGUI

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see neaGUI. An R package to perform the network enrichment analysis (NEA). Bioconductor version: 2.13 neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko…

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Bioconductor – SNPRelate

DOI: 10.18129/B9.bioc.SNPRelate     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SNPRelate. Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data Bioconductor version: 3.12 Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and…

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Bioconductor – atena

DOI: 10.18129/B9.bioc.atena     Analysis of Transposable Elements Bioconductor version: Release (3.14) Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification…

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Bioconductor – STATegRa (development version)

DOI: 10.18129/B9.bioc.STATegRa     This is the development version of STATegRa; for the stable release version, see STATegRa. Classes and methods for multi-omics data integration Bioconductor version: Development (3.15) Classes and tools for multi-omics data integration. Author: STATegra Consortia Maintainer: David Gomez-Cabrero <david.gomezcabrero at ki.se>, Núria Planell <nuria.planell.picola at navarra.es>…

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Bioconductor – Roberts2005Annotation.db (development version)

DOI: 10.18129/B9.bioc.Roberts2005Annotation.db     This is the development version of Roberts2005Annotation.db; for the stable release version, see Roberts2005Annotation.db. Roberts2005Annotation Annotation Data (Roberts2005Annotation) Bioconductor version: Development (3.15) Roberts2005Annotation Annotation Data (Roberts2005Annotation) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R,…

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Bioconductor – interactiveDisplay

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see interactiveDisplay. Package for enabling powerful shiny web displays of Bioconductor objects Bioconductor version: 3.2 The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects. Author: Shawn…

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Bioconductor – rgsepd

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see rgsepd. Gene Set Enrichment / Projection Displays Bioconductor version: 3.4 R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential…

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Bioconductor – Harman

DOI: 10.18129/B9.bioc.Harman     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Harman. The removal of batch effects from datasets using a PCA and constrained optimisation based technique Bioconductor version: 3.12 Harman is a PCA and constrained optimisation based technique that maximises the…

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Bioconductor – VanillaICE

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see VanillaICE. A Hidden Markov Model for high throughput genotyping arrays Bioconductor version: 3.4 Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays. Author: Robert Scharpf <rscharpf at jhu.edu>, Kevin Scharpf,…

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Bioconductor – ChIPComp

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ChIPComp. Quantitative comparison of multiple ChIP-seq datasets Bioconductor version: 3.4 ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control. Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang Maintainer:…

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Bioconductor – systemPipeRdata

DOI: 10.18129/B9.bioc.systemPipeRdata     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata. systemPipeRdata: NGS workflow templates and sample data Bioconductor version: 3.9 systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used…

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Bioconductor – ramr

DOI: 10.18129/B9.bioc.ramr     Detection of Rare Aberrantly Methylated Regions in Array and NGS Data Bioconductor version: Release (3.13) ramr is an R package for detection of low-frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. In addition, package provides functions…

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Bioconductor – fcScan

DOI: 10.18129/B9.bioc.fcScan     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see fcScan. fcScan for detecting clusters of coordinates with user defined options Bioconductor version: 3.12 This package is used to detect combination of genomic coordinates falling within a user defined window size…

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List of all packages in BioConductor transition dependency level 1 failing due issue with either RUnit or testthat)

Hi, thanks to several hints I was able to nearly solve all issues. On Thu, Sep 02, 2021 at 01:12:29PM +0200, Andreas Tille wrote: > > The packages in question are mentioned as Test-Depends and I have no > idea why these are not found. It was solved by accorcing…

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Bioconductor – netbenchmark

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see netbenchmark. Benchmarking of several gene network inference methods Bioconductor version: 3.4 This package implements a benchmarking of several gene network inference algorithms from gene expression data. Author: Pau Bellot, Catharina Olsen, Patrick Meyer,…

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List of all packages in BioConductor transition dependency level 1 failing due issue with either RUnit or testthat

Hi Andreas, On 02-09-2021 13:12, Andreas Tille wrote: > I did added an info about all those packages of level 1 that are failing > either due to RUnit or testthat issues and here is a manually edited > `grep -A8 ‘/jobs/’ r-bioc-*/debian/changelog` on my local disk: > > r-bioc-biocparallel/debian/changelog:…

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