Tag: RUnit

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…

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…

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>…

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…

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”)):…

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…

    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)…

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…

    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…

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…

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…

    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…

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…

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…

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…

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…

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…

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…

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…

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:…

    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…

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…

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…

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>…

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,…

    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…

    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…

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…

    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,…

    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:…

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…

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…

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…

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…

    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,…

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:…