Tag: Bioconductor

Bioconductor – Resourcerer

Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. Bioconductor version: 2.6 This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package. Author:…

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Bioconductor – edge

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see edge. Extraction of Differential Gene Expression Bioconductor version: 3.2 The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and…

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Bioconductor – topGO

topGO: Enrichment analysis for Gene Ontology Bioconductor version: 2.6 topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. Author: Adrian Alexa, Jorg…

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Bioconductor – SSPA

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see SSPA. General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data Bioconductor version: 3.0 General Sample size and power analysis for microarray and next-generation sequencing data. Author: Maarten van Iterson Maintainer:…

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Bioconductor – CGHcall

Calling aberrations for array CGH tumor profiles. Bioconductor version: 2.6 Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided. Author: Sjoerd Vosse and Mark van de Wiel Maintainer: Mark…

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NFP: Network fingerprint analysis in R

This package implements the network fingerprint framework. A biomedical network is characterized as a spectrum-like vector called “network fingerprint”, which contains similarities to basic networks. This knowledge-based multidimensional characterization provides a more intuitive way to decipher molecular networks, especially for large-scale network comparisons and clustering analyses Prerequisites NFP is free…

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Treat time variable as continuous or discrete?

Hello, I have two questions regarding an RNA-seq experiment with 10 time points and 20 replicates per time point. So far I’ve run an LRT using the following models: design = ~ timepoint reduced = ~ 1 Throughout the experiment, RNA was extracted at days 3, 4, 15, 16, 44,…

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Bioconductor – epistack (development version)

DOI: 10.18129/B9.bioc.epistack     This is the development version of epistack; for the stable release version, see epistack. Heatmaps of Stack Profiles from Epigenetic Signals Bioconductor version: Development (3.15) The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq,…

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corral: Single-cell RNA-seq dimension reduction, batch integration, and visualization with correspondence analysis

Abstract Effective dimension reduction is an essential step in analysis of single cell RNA-seq(scRNAseq) count data, which are high-dimensional, sparse, and noisy. Principal component analysis (PCA) is widely used in analytical pipelines, and since PCA requires continuous data, it is often coupled with log-transformation in scRNAseq applications. However, log-transformation of…

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Bioconductor – HEM

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see HEM. Heterogeneous error model for identification of differentially expressed genes under multiple conditions Bioconductor version: 2.9 This package fits heterogeneous error models for analysis of microarray data Author: HyungJun Cho <hcho at virginia.edu>…

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Bioconductor – nudge

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see nudge. Normal Uniform Differential Gene Expression detection Bioconductor version: 2.9 Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the…

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Bioconductor – xtropicaliscdf

DOI: 10.18129/B9.bioc.xtropicaliscdf     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see xtropicaliscdf. xtropicaliscdf Bioconductor version: 3.13 A package containing an environment representing the X_tropicalis.cdf file. Author: The Bioconductor Project Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“xtropicaliscdf”)):…

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Bioconductor – rgu34cprobe

DOI: 10.18129/B9.bioc.rgu34cprobe     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see rgu34cprobe. Probe sequence data for microarrays of type rgu34c Bioconductor version: 3.10 This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from www.affymetrix.com. The…

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Bioconductor – geneplotter

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see geneplotter. Graphics related functions for Bioconductor Bioconductor version: 2.9 Some basic functions for plotting genetic data Author: R. Gentleman, Biocore Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“geneplotter”)):…

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Bioconductor – pint

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see pint. Pairwise INTegration of functional genomics data Bioconductor version: 2.9 Pairwise data integration for functional genomics. In particular, tools to screen functionally active chromosomal aberrations from paired copy number, gene expression and miRNA…

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Bioconductor – pint

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see pint. Pairwise INTegration of functional genomics data Bioconductor version: 2.9 Pairwise data integration for functional genomics. In particular, tools to screen functionally active chromosomal aberrations from paired copy number, gene expression and miRNA…

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Bioconductor – pathRender

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see pathRender. Render molecular pathways Bioconductor version: 2.9 build graphs from pathway databases, render them by Rgraphviz Author: Li Long <lilong at isb-sib.ch> Maintainer: Li Long <lilong at isb-sib.ch> Citation (from within R, enter…

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Bioconductor – pathRender

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see pathRender. Render molecular pathways Bioconductor version: 2.9 build graphs from pathway databases, render them by Rgraphviz Author: Li Long <lilong at isb-sib.ch> Maintainer: Li Long <lilong at isb-sib.ch> Citation (from within R, enter…

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High-Throughput RNA Sequencing Reveals the Effect of NB-UVB

Introduction Psoriasis vulgaris, major chronic immune-mediated skin disease, affects 1–3% of the adult population worldwide.1 Psoriasis is one of the major complex skin diseases that is significantly linked to genetic predisposition, major histocompatibility alleles, and environmental factors.2 Over the past few years, the cellular and molecular contributions to psoriasis were…

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Bioconductor – svaRetro

DOI: 10.18129/B9.bioc.svaRetro     Retrotransposed transcript detection from structural variants Bioconductor version: Release (3.14) svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported…

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From DNA sequences to microbial ecology: Wrangling NEON soil microbe data with the neonMicrobe R package – Qin – 2021 – Ecosphere

Introduction Microbial life on earth is ubiquitous and essential in critical ecosystem processes (Cavicchioli et al. 2019). Soils are among the most diverse microbial habitats known, and recent surveys at continental (Fierer et al. 2012, Ladau et al. 2013, Talbot et al. 2014, Prober et al. 2015, Thompson et al. 2017, Wang et al. 2018) and global…

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Computational Biologist, Clinical Bioinformatics – Remote

The NGS Bioinformatics Group at Dana-Farber Cancer Institute seeks a Computational Biologist to work on Profile, our institutional comprehensive precision cancer medicine initiative. The candidate will work on developing NGS bioinformatic workflows and modules for the analysis of rich and complex somatic and germline data from the Profile project and…

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Computational Biologist, Clinical Bioinformatics – Remote

The NGS Bioinformatics Group at Dana-Farber Cancer Institute seeks a Computational Biologist to work on Profile, our institutional comprehensive precision cancer medicine initiative. The candidate will work on developing NGS bioinformatic workflows and modules for the analysis of rich and complex somatic and germline data from the Profile project and…

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Bioconductor – rsbml

DOI: 10.18129/B9.bioc.rsbml     R support for SBML, using libsbml Bioconductor version: Release (3.5) Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models. Author: Michael Lawrence <michafla…

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Bioconductor – GenomeInfoDb

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see GenomeInfoDb. Utilities for manipulating chromosome and other ‘seqname’ identifiers Bioconductor version: 3.2 Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., “chr1” versus “1”), including a…

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Bioconductor – GenomeInfoDb

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see GenomeInfoDb. Utilities for manipulating chromosome and other ‘seqname’ identifiers Bioconductor version: 3.2 Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., “chr1” versus “1”), including a…

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Bioconductor – Rredland

interface to redland RDF utilities Bioconductor version: 2.6 interface to redland RDF utilities; assumes librdf, possibly berkeley DB; include OWL files from www.biopax.org, and RDF serializations of various resources from ISB-SIB.CH; redland is a production of Dave Beckett (see librdf.org) Author: VJ Carey <stvjc at channing.harvard.edu> Maintainer: VJ Carey <stvjc…

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Bowtie2 alignment using a large index (*.bt2l)

Bowtie2 alignment using a large index (*.bt2l) 0 Hello! I have used Bowtie2 to in the past successfully to index and align reads on R. I currently have a job that requires using large index. bowtie2_build returns successful index, but it has the unique bt2l extension (as mention in bowtie2…

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Bioconductor – ChIPXpressData

DOI: 10.18129/B9.bioc.ChIPXpressData     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see ChIPXpressData. ChIPXpress Pre-built Databases Bioconductor version: 3.11 Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking. Author: George Wu Maintainer: George Wu…

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Bioconductor – ChromHeatMap

DOI: 10.18129/B9.bioc.ChromHeatMap     Heat map plotting by genome coordinate Bioconductor version: Release (3.5) The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes…

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Bioconductor – cytofast

DOI: 10.18129/B9.bioc.cytofast     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 cytofast. cytofast…

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Bioconductor – coRNAi

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see coRNAi. Analysis of co-knock-down RNAi data Bioconductor version: 2.12 Analysis of combinatorial cell-based RNAi screens Author: Elin Axelsson Maintainer: Elin Axelsson <elin.axelsson at imp.ac.at> Citation (from within R, enter citation(“coRNAi”)): Installation To install…

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Bioconductor – msPurity

DOI: 10.18129/B9.bioc.msPurity     Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics Bioconductor version: Release (3.5) Assess the contribution of the targeted precursor in fragmentation acquired or anticipated isolation windows using a metric called “precursor purity”. Also provides simple processing steps (averaging, filtering, blank subtraction,…

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Bioconductor – GSE159526

DOI: 10.18129/B9.bioc.GSE159526     Placental cell DNA methylation data from GEO accession GSE159526 Bioconductor version: Release (3.14) 19 term and 9 first trimester placental chorionic villi and matched cell-sorted samples ran on Illumina HumanMethylationEPIC DNA methylation microarrays. This data was made available on GEO accession [GSE159526](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159526). Both the raw and…

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Bioconductor – pRoloc

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see pRoloc. A unifying bioinformatics framework for spatial proteomics Bioconductor version: 3.0 This package implements pattern recognition techniques on quantitiative mass spectrometry data to infer protein sub-cellular localisation. Author: Laurent Gatto and Lisa M….

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Bioconductor – pRoloc

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see pRoloc. A unifying bioinformatics framework for spatial proteomics Bioconductor version: 3.0 This package implements pattern recognition techniques on quantitiative mass spectrometry data to infer protein sub-cellular localisation. Author: Laurent Gatto and Lisa M….

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no DE genes found in subset

Troubleshooting DESeq2 Analysis: no DE genes found in subset 1 @8e2958c3 Last seen 5 hours ago United States Hi, I’m quite new to R and DESeq2 and need some help troubleshooting! I’m working on analyzing a dataset comparing 3 groups: patients before and after a treatment against a healthy control…

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Bioconductor – netresponse

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see netresponse. NetResponse: functional network analysis Bioconductor version: 2.12 Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling. Author: Leo Lahti, Olli-Pekka Huovilainen,…

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Bioconductor – netresponse

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see netresponse. NetResponse: functional network analysis Bioconductor version: 2.12 Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling. Author: Leo Lahti, Olli-Pekka Huovilainen,…

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Gene Id Conversion Tool

MyGene.info is a web service that provides up to date annotations in several fields and is great for gene ID conversion. All species from NCBI and Ensembl are supported and annotations are updated weekly to ensure the latest annotations are available. Both python and R/Bioconductor clients are easy to use….

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Bioconductor – CRImage

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see CRImage. CRImage a package to classify cells and calculate tumour cellularity Bioconductor version: 2.12 CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the…

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Bioconductor – RnBeads.hg19

DOI: 10.18129/B9.bioc.RnBeads.hg19     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RnBeads.hg19. RnBeads.hg19 Bioconductor version: 3.9 Automatically generated RnBeads annotation package for the assembly hg19. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator <rnbeads at mpi-inf.mpg.de> Citation (from within R, enter citation(“RnBeads.hg19”)): Installation To install this…

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Bioconductor – dStruct

DOI: 10.18129/B9.bioc.dStruct     Identifying differentially reactive regions from RNA structurome profiling data Bioconductor version: Release (3.14) dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al, Genome Biology,…

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Bioconductor – genoset

    This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see genoset. Provides classes similar to ExpressionSet for copy number analysis Bioconductor version: 2.8 Load, manipulate, and plot copynumber and BAF data. GenoSet class extends eSet by adding a “locData” slot for a RangedData…

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WGCNA Analysis Identifies Polycystic Ovary Syndrome-Associated Circula

Introduction Polycystic ovary syndrome (PCOS) is a common endocrine metabolic disorder in women of childbearing age.1 PCOS patients are typically characterized by androgen excess, polycystic ovaries and anovulation, and are often accompanied by insulin resistance and obesity.2 Consequently, patients with this syndrome not only suffer from infertility,3 but also have…

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Bioconductor – weaver

    This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see weaver. Tools and extensions for processing Sweave documents Bioconductor version: 2.10 This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is…

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Bioconductor – tuberculosis

DOI: 10.18129/B9.bioc.tuberculosis     Tuberculosis Gene Expression Data for Machine Learning Bioconductor version: Release (3.14) The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been…

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Bioconductor – BeadDataPackR

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see BeadDataPackR. Compression of Illumina BeadArray data Bioconductor version: 2.12 Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform Author: Mike Smith, Andy Lynch Maintainer: Mike Smith…

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Bioconductor – rBiopaxParser

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see rBiopaxParser. Parses BioPax files and represents them in R Bioconductor version: 3.3 Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported. Author: Frank…

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Bioconductor Traviz :: Anaconda.org

Description traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in reduced dimension, as well as averge gene expression smoothers as a function of pseudotime. Asides from general utility functions, traviz also allows plotting trajectories estimated by Slingshot, as well as…

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Bioconductor – IntramiRExploreR

DOI: 10.18129/B9.bioc.IntramiRExploreR     This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see IntramiRExploreR. Predicting Targets for Drosophila Intragenic miRNAs Bioconductor version: 3.7 Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using…

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Elastic Net for RNAseq data

Elastic Net for RNAseq data 1 @1c386ab3 Last seen 1 hour ago Canada I have RNAseq results from NovaSeq and after doing some differential gene expression with DESeq2, I will like to explore the Elastic Net model to select features that differentiate my two conditions. However, I haven’t been able…

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Deseq2 model matrix error

Deseq2 model matrix error 1 I have trying to do Deseq2 analysis for mainly mutants vs controls. I have two covariates influencing the dataset – Gender and Genotype. This is how my sample annotation file looks – sample condition genotype gender SK01 mutant hr F SK02 mutant hr F SK03…

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Permanent error in installing GenomeInfoDb

Permanent error in installing GenomeInfoDb 1 @fereshteh-15803 Last seen 1 hour ago United Kingdom Hello I am not able to install GenomeInfoDb Can you help me please? > remotes::install_github(“Bioconductor/GenomeInfoDb”) Downloading GitHub repo Bioconductor/GenomeInfoDb@HEAD ✓ checking for file ‘/tmp/Rtmp4he3Nm/remotese273c245ce2/Bioconductor-GenomeInfoDb-d4604b1/DESCRIPTION’ … ─ preparing ‘GenomeInfoDb’: ✓ checking DESCRIPTION meta-information … ─ checking for…

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zellkonverter from monahton – Github Help

zellkonverter is a small package for converting between SingleCellExperiment objects and alternative objects for storing single-cell RNA-sequencing data (such as AnnData). It is built on top of the basilisk package. For documentation see please refer to Bioconductor. Development documentation is also available on Bioconductor devel or the pkgdown site. Installation…

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Bioconductor – PWMEnrich.Mmusculus.background

DOI: 10.18129/B9.bioc.PWMEnrich.Mmusculus.background     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see PWMEnrich.Mmusculus.background. M. musculus background for PWMEnrich Bioconductor version: 3.11 PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs. Author: Robert Stojnic Maintainer: Robert Stojnic <robert.stojnic at gmail.com> Citation…

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PCA plot from read count matrix from RNA-Seq

NB – this is now a Bioconductor R package: github.com/kevinblighe/PCAtools ————————- You should normalise your data prior to performing PCA. In the code below, you’ll have to add plot legends yourself, and also colour vectors (passed to the ‘col‘ parameter). Then, assuming that you have transcripts as rows and samples…

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PCA plot from read count matrix from RNA-Seq

NB – this is now a Bioconductor R package: github.com/kevinblighe/PCAtools ————————- You should normalise your data prior to performing PCA. In the code below, you’ll have to add plot legends yourself, and also colour vectors (passed to the ‘col‘ parameter). Then, assuming that you have transcripts as rows and samples…

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Interploidy gene flow involving the sexual-asexual cycle facilitates the diversification of gynogenetic triploid Carassius fish

1. Muller, H. J. The relation of recombination to mutational advance. Mutat. Res. Mol. Mech. Mutagen. 1, 2–9 (1964). Google Scholar  2. Maynard Smith, J. The Evolution of Sex (Cambridge University Press, 1978). Google Scholar  3. Avise, J. C. Clonality (Oxford University Press, 2008). Google Scholar  4. Hamilton, W. D.,…

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BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction

doi: 10.1007/s10142-021-00821-9. Online ahead of print. Affiliations Expand Affiliations 1 Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego 2000, P5, sala 217, Campos dos Goytacazes, RJ, Brazil. fabricio_almeidasilva@hotmail.com. 2 Laboratório de Química e Função…

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BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction

doi: 10.1007/s10142-021-00821-9. Online ahead of print. Affiliations Expand Affiliations 1 Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego 2000, P5, sala 217, Campos dos Goytacazes, RJ, Brazil. fabricio_almeidasilva@hotmail.com. 2 Laboratório de Química e Função…

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Bioconductor – BSgenome.Mmusculus.UCSC.mm39

DOI: 10.18129/B9.bioc.BSgenome.Mmusculus.UCSC.mm39     Full genome sequences for Mus musculus (UCSC genome mm39, based on GRCm39) Bioconductor version: Release (3.14) Full genome sequences for Mus musculus (Mouse) as provided by UCSC (genome mm39, based on assembly GRCm39) and stored in Biostrings objects. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package…

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the standard deviation is zero”

Hi, I am following RnBeads tutorial and with Ziller2011_PLoSGen_450K data set. The tutorial says that the analysis takes 1 1/2 hours on two compute nodes but for me after overnight run with 4 cores it didn’t finish so I had to terminate the process. It seems that there is a…

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Chapter 9 The CITATION file

Appropriate citations must be included in help pages (e.g., in the see also section) and vignettes; this aspect of documentation is no different from any scientific endeavor. The file inst/CITATION can be used to specify how a package is to be cited. If this option is utilized, a maintainer can…

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Bioconductor – cageminer

DOI: 10.18129/B9.bioc.cageminer     Candidate Gene Miner Bioconductor version: Release (3.14) This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally,…

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Bioconductor – MSMB

DOI: 10.18129/B9.bioc.MSMB     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see MSMB. Data sets for the book ‘Modern Statistics for Biology’ Bioconductor version: 3.8 Data sets for the book ‘Modern Statistics for Modern Biology’, S.P. Holmes and W. Huber. Author: Wolfgang Huber,…

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Bioconductor – xenopus.db0

DOI: 10.18129/B9.bioc.xenopus.db0     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see xenopus.db0. Base Level Annotation databases for xenopus Bioconductor version: 3.12 Base annotation databases for xenopus, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. Author: Bioconductor Core Team…

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Bioconductor – BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor

DOI: 10.18129/B9.bioc.BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor     Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected minor alleles (dbSNP151) Bioconductor version: Release (3.14) Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings…

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Bioinformatics Scientist in Cambridge, Cambridgeshire | Cpl Life Sciences

Bioinformatics Scientist OUTSIDE IR35 12 month contract 25 per hour LTD Skills: NGS data analyses on Unix platforms, Python Typical Accountabilities Management of data exchange with collaborators, ingestion, annotation and making the genomics datasets analysis ready. Deployment and support of Precision Medicine & Biosamples data analysis software and bioinformatic workflows…

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mdozmorov/conference_template: Bioconductor conference template web site

GitHub – mdozmorov/conference_template: Bioconductor conference template web site You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here: Source link

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Bioconductor – htratfocus.db

DOI: 10.18129/B9.bioc.htratfocus.db     Affymetrix Affymetrix HT_Rat-Focus Array annotation data (chip htratfocus) Bioconductor version: Release (3.14) Affymetrix Affymetrix HT_Rat-Focus Array annotation data (chip htratfocus) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“htratfocus.db”)): Installation To install this…

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Bioconductor – goseq

    This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see goseq. Gene Ontology analyser for RNA-seq and other length biased data Bioconductor version: 2.10 Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data Author: Matthew Young Maintainer:…

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Bioconductor – goseq

    This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see goseq. Gene Ontology analyser for RNA-seq and other length biased data Bioconductor version: 2.10 Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data Author: Matthew Young Maintainer:…

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Bioconductor – IHWpaper

DOI: 10.18129/B9.bioc.IHWpaper     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see IHWpaper. Reproduce figures in IHW paper Bioconductor version: 3.11 This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (www.nature.com/articles/nmeth.3885) and the latest arXiv preprint available…

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Bioconductor – TabulaMurisData

DOI: 10.18129/B9.bioc.TabulaMurisData     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see TabulaMurisData. 10x And SmartSeq2 Data From The Tabula Muris Consortium Bioconductor version: 3.10 Access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium…

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Downgrade R version and R package Bioconductor [duplicate]

If my Bioconductor packages were installed in the R home directory, then I’d remove.packages() instead of setting .libPaths(), or I’d run BiocInstaller::biocValid() and follow the directions for reverting “too new” packages.,Generally, Bioconductor is designed to work with specific versions of R, so there are no guarantees associated with using older…

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Bioconductor – quantsmooth

Quantile smoothing and genomic visualization of array data Bioconductor version: 2.6 Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53. Author: Jan Oosting, Paul Eilers, Renee Menezes Maintainer: Jan Oosting <j.oosting at lumc.nl> To install this package, start…

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Bioconductor – quantsmooth

Quantile smoothing and genomic visualization of array data Bioconductor version: 2.6 Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53. Author: Jan Oosting, Paul Eilers, Renee Menezes Maintainer: Jan Oosting <j.oosting at lumc.nl> To install this package, start…

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Bioconductor – cellHTS2

Analysis of cell-based screens – revised version of cellHTS Bioconductor version: 2.5 Analysis of cell-based RNA interference screens. See ?cellHTS2 for a brief introduction. Author: Ligia Bras <ligia at ebi.ac.uk>, Wolfgang Huber <huber at ebi.ac.uk>, Michael Boutros <m.boutros at dkfz.de>, Gregoire Pau <gpau at ebi.ac.uk>, Florian Hahne <fhahne at fhcrc.org>…

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Bioconductor – cellHTS2

Analysis of cell-based screens – revised version of cellHTS Bioconductor version: 2.5 Analysis of cell-based RNA interference screens. See ?cellHTS2 for a brief introduction. Author: Ligia Bras <ligia at ebi.ac.uk>, Wolfgang Huber <huber at ebi.ac.uk>, Michael Boutros <m.boutros at dkfz.de>, Gregoire Pau <gpau at ebi.ac.uk>, Florian Hahne <fhahne at fhcrc.org>…

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100% Postdoctoral Position in Bioinformatics to study Gene Regulatory Networks – University of Basel – job portal

100% Postdoctoral Position in Bioinformatics to study Gene Regulatory Networks 2-2.5 year fixed-term contract available immediately or as agreed Understanding how a fertilized egg develops into a complex multicellular organism is one of the most fascinating topics in biology. The current challenge is to understand how genes function as part…

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Bioconductor/BiocAnVIL: prototypical project pkgdown site for BioC work on AnVIL

GitHub – Bioconductor/BiocAnVIL: prototypical project pkgdown site for BioC work on AnVIL You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here: Source…

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r – GDCprepare() returns Error in function (classes, fdef, mtable)

I have downloaded Proteome Profiling data from the TCGA-LGG project with the Bioconductor package TCGAbiolinks. Then I have the following error when running GDCprepare: library(“TCGAbiolinks”) query_lgg = GDCquery( project = “TCGA-LGG”, data.category = “Proteome Profiling”, sample.type = “Primary Tumor”, legacy = FALSE) #> ————————————– #> o GDCquery: Searching in GDC…

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Error using getGEO – error reading from the connection

Error using getGEO – error reading from the connection 0 Hi, I’ve been trying to open GEO data in R studio. So far I have the following code, copied from a tutorial: #tutorial for analysing data from GEO library(GEOquery) my_id <- “GSE33126” gse <- getGEO(my_id) However, I get the following…

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Problem loading R packages on MacBook Pro

Problem loading R packages on MacBook Pro 1 @7702478d Last seen 15 minutes ago South Africa Hi everyone I am new to using MacOS for R packages. I have recently purchased a MacBook Pro M1 with BigSur OS. My initial attempts to just use R were met with frustration and…

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Bioconductor – mosbi

DOI: 10.18129/B9.bioc.mosbi     Molecular Signature identification using Biclustering Bioconductor version: Release (3.14) This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters…

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Bioconductor – hca

DOI: 10.18129/B9.bioc.hca     Exploring the Human Cell Atlas Data Coordinating Platform Bioconductor version: Release (3.14) This package provides users with the ability to query the Human Cell Atlas data repository for single-cell experiment data. The `projects()`, `files()`, `samples()` and `bundles()` functions retrieve summary information on each of these indexes;…

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How to introduce mutations to protein Fasta sequences in R?

How to introduce mutations to protein Fasta sequences in R? 0 Dear all, I have a list of genes, for which I have retrieved the UniProt protein sequences. I want to retrieve the sequence of particular mutations to the protein sequences, for example W155L, and save it in fasta format….

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Bioconductor – pepDat

DOI: 10.18129/B9.bioc.pepDat     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see pepDat. Peptide microarray data package Bioconductor version: 3.9 Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. Author: Renan…

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Bioinformatics Scientist II in Philadelphia, Pennsylvania

Location: LOC_ABRAMSON-Abramson Building  Req ID: 153191 Shift: Any Employment Status: Regular – Full Time  Job Summary The Bioinformatics Scientist II position is an entry level position for a PhD level professional and a 2nd stage position for those with moderate experience without a PhD. The focus of the position is service-level application of…

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Bioconductor – zinbwave

DOI: 10.18129/B9.bioc.zinbwave     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see zinbwave. Zero-Inflated Negative Binomial Model for RNA-Seq Data Bioconductor version: 3.12 Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell…

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Bioconductor – BgeeCall

DOI: 10.18129/B9.bioc.BgeeCall     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see BgeeCall. Automatic RNA-Seq present/absent gene expression calls generation Bioconductor version: 3.12 BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM Author: Julien Wollbrett [aut, cre],…

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Bioconductor – MetaboSignal (development version)

DOI: 10.18129/B9.bioc.MetaboSignal     This is the development version of MetaboSignal; for the stable release version, see MetaboSignal. MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways Bioconductor version: Development (3.15) MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG…

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Bioconductor – AIMS (development version)

DOI: 10.18129/B9.bioc.AIMS     This is the development version of AIMS; for the stable release version, see AIMS. AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype Bioconductor version: Development (3.15) This package contains the AIMS implementation. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal…

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Issue with annotation package mouse4302.db

Issue with annotation package mouse4302.db 1 @1449e5ac Last seen 7 hours ago United States Hi All, I am trying to install mouse4302.db annotation package. I get a syntax error (see below). I tried installing using the tar.gz package too, but had the same result. Can anyone provide me a workaround…

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Bioconductor – clariomshumanhttranscriptcluster.db

DOI: 10.18129/B9.bioc.clariomshumanhttranscriptcluster.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see clariomshumanhttranscriptcluster.db. Affymetrix clariomshumanht annotation data (chip clariomshumanhttranscriptcluster) Bioconductor version: 3.11 Affymetrix clariomshumanht annotation data (chip clariomshumanhttranscriptcluster) assembled using data from public repositories Author: James W. MacDonald Maintainer: Biocore Package Maintainer <maintainer…

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DNA methylation batch effect remove

DNA methylation batch effect remove 1 Hi, I’m studying about DNA methylation. I draw heatmap with beta-value, but there are batch effects.. How can I remove these cgID with studio R? DNA effect batch methylation • 24 views Can you explain what do you mean by ‘beta-value’? Generally batch effect…

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Bioconductor – RTCGA.mRNA

DOI: 10.18129/B9.bioc.RTCGA.mRNA     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see RTCGA.mRNA. mRNA datasets from The Cancer Genome Atlas Project Bioconductor version: 3.11 Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from gdac.broadinstitute.org/. Data format…

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Bioconductor – bgafun

    This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see bgafun. BGAfun A method to identify specifity determining residues in protein families Bioconductor version: 2.8 A method to identify specifity determining residues in protein families using Between Group Analysis Author: Iain Wallace Maintainer:…

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Bioconductor – org.Xl.eg.db

DOI: 10.18129/B9.bioc.org.Xl.eg.db     This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see org.Xl.eg.db. Genome wide annotation for Xenopus Bioconductor version: 3.7 Genome wide annotation for Xenopus, primarily based on mapping using Entrez Gene identifiers. Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at…

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