Tag: Bioconductor

InteractiveComplexHeatmap on DESeq2 object with more than 2 groups

InteractiveComplexHeatmap on DESeq2 object with more than 2 groups 1 Hello all, I’m writing with the hope someone can clarify a doubt I have about the differential heatmap generated by the package InteractiveComplexHeatmap via the simple command interactivate(dds). I read the package documentation at bioconductor.org/packages/release/bioc/html/InteractiveComplexHeatmap.html, but I couldn’t find the…

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MND1 Expression as a Predictor of Breast Cancer Survival

Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…

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Unsuccessful DE analysis using limma

This might be a bit long, please bare with me. I’m conducting a differential expression analysis using limma – voom. My comparison is regarding response vs non-response to a cancer drug. However, I’m not getting any DE genes, absolute zeros. Someone here once recommended not to use contrast matrix for…

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Bioconductor – htrat230pmprobe

DOI: 10.18129/B9.bioc.htrat230pmprobe     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see htrat230pmprobe. Probe sequence data for microarrays of type htrat230pm Bioconductor version: 3.14 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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Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics

Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…

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Bioconductor – RAREsim

DOI: 10.18129/B9.bioc.RAREsim     Simulation of Rare Variant Genetic Data Bioconductor version: Release (3.15) Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins – either as provided by default parameters or estimated from…

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Bioconductor – AHEnsDbs

DOI: 10.18129/B9.bioc.AHEnsDbs     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see AHEnsDbs. EnsDbs for AnnotationHub Bioconductor version: 3.10 Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species. EnsDb SQLite databases are generated separately from Ensembl MySQL databases using functions from the…

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Bioconductor – bladderbatch

DOI: 10.18129/B9.bioc.bladderbatch     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see bladderbatch. Bladder gene expression data illustrating batch effects Bioconductor version: 3.12 This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an…

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Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

Job details Job type full-time Full job description Location: loc_roberts-roberts ctr pediatric research req id: 134035 shift: days employment status: regular – full time job summary the bioinformatics unit (bixu) within the center for data driven discovery (d3b) at the children’s hospital of philadelphia (chop) is seeking a level iii…

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CRISPRi for specific inhibition of miRNA clusters and miRNAs with high sequence homology

Bartel, D. P. MicroRNAs: Target recognition and regulatory functions. Cell 136, 215–233 (2009). CAS  Article  Google Scholar  Bassett, A. R. et al. Understanding functional miRNA–target interactions in vivo by site-specific genome engineering. Nat. Commun. 5, 4640 (2014). ADS  CAS  Article  Google Scholar  Moore, M. J. et al. miRNA–target chimeras reveal…

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Bioconductor – synaptome.data

DOI: 10.18129/B9.bioc.synaptome.data     AnnotationData for Synaptome.DB package Bioconductor version: Release (3.14) The package provides access to the copy of the Synaptic proteome database. It was designed as an accompaniment for Synaptome.DB package. Database provides information for specific genes and allows building the protein-protein interaction graph for gene sets, synaptic…

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scrnaseq – Normalization methods to combine scRNA-seq experiments with different sequencing depths

I don’t think you need to complicate the idea of normalisation by introducing machine learning classifiers as a necessary component. Normalisation is common when comparing different datasets for all differential analysis. If you have single cell data, have a look at integration techniques in the Seurat workflows: satijalab.org/seurat/articles/integration_rpca.html If you’ve…

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3 arguments passed to .Internal(is.unsorted) which requires 2 #95

Kevinrue I am getting this error, using R 4.2.0 and Bioconductor 3.15: library(scRNAseq) > sce <- HermannSpermatogenesisData() […] Error in ..Internal(is.unsorted(x, FALSE, FALSE)) : 3 arguments passed to .Internal(is.unsorted) which requires 2 I’ve chased the issue down to this line (and the next) github.com/Bioconductor/S4Vectors/blob/338534bfb5fb6ada3f2abc144017bc8ce0aab6c3/R/isSorted.R#L149 That’s as far as I managed…

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bioconductor – Unable to install GEOquery

I just installed Bioconductor in RStudio 4.1.1: if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) I am currently trying to install GEOquery package from Bioconductor but it is throwing error messages and I don’t know what the problem is or how to fix it: BiocManager::install(“GEOquery”) Error Message: ‘getOption(“repos”)’ replaces Bioconductor standard repositories,…

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Install Bioconductor package using rpy2 in Python Jupyter notebook

This introduction comes from this SO question: “argument is of length zero” is a very specific problem that comes from one of my least-liked elements of R. Let me demonstrate the problem: > FALSE == “turnip” [1] FALSE > TRUE == “turnip” [1] FALSE > NA == “turnip” [1] NA…

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Bioconductor – Rsubread

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see Rsubread. Rsubread: high-performance read alignment, quantification and mutation discovery Bioconductor version: 2.13 This R package provides easy-to-use tools for analyzing next-gen sequencing read data. Functions of these tools include quality assessment, read alignment,…

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Bioconductor – keggorthology

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see keggorthology. graph support for KO, KEGG Orthology Bioconductor version: 2.13 graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused…

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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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adRn-s/ukbbgwas – githubhot

Explore SNVs associations with traits of UK BioBank. GWAS study results where made publicly available courtesy of Neale’s Lab on August 1st, 2018. For more information please visit: www.nealelab.is/uk-biobank INSTALL In R: devtools::install_github(“adRn-s/ukbbgwas”). DEV(s) Dependencies Mandatory and optional dependencies can all be handled with bioconda. Here’s a complete YAML specification…

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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 – illuminaRatv1.db

DOI: 10.18129/B9.bioc.illuminaRatv1.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see illuminaRatv1.db. Illumina Ratv1 annotation data (chip illuminaRatv1) Bioconductor version: 3.11 Illumina Ratv1 annotation data (chip illuminaRatv1) assembled using data from public repositories Author: Mark Dunning, Andy Lynch, Matthew Eldridge Maintainer: Mark…

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Postdoctoral Position in Bioinformatics to study Gene Regulatory Networks

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 of gene regulatory networks (GRNs) that control the proliferation and patterning of progenitor and stem cells during embryonic development….

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R package with CRAN and Bioconductor dependencies

The short answer: setRepositories(ind=1:2) tl;dr The documentation for setRepositories tells us that the “default list of known repositories is stored in the file ‘R_Home/etc/repositories’”. We can track this down a couple of ways, but for convenience, let’s read the table of repositories into R (this will cut off all of…

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licensing – Properly License R Package that Depends on Package from Bioconductor that Imposes Restrictions

I have a problem choosing the right license for my package. My package flowdex depends on some packages from Bioconductor, among them flowWorkspace. flowWorkspace has a file license that says, in short, “academic research only and non-commercial“. Now the question is what license to use in my package flowdex? If…

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Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis

Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS  Google Scholar  Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…

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Bioconductor installation problems

Dear Friends, I have been having considerable difficulty doing various package related bioconductor actions. Here is my system specifications: ======================================================================= macOS Monterey Version: 12.3 (21E230) MacBook Pro (Retina, 13-inch, Early 2015) Memory: 16 GB 1867 MHz DDR3 RStudio 2021.09.0 Build 351 R version 4.1.2 (2021-11-01) — “Bird Hippie” Copyright (C)…

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AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required

Hello, I am currently trying to install AnnotationHub but I am running into problems. I use R 4.0.4, renv (version 0.15.4) and BiocVersion 3.12. When I run BiocManager::install(“AnnotationHub”), I get the following error: Warning message: This project is configured to use R version ‘4.1.1’, but ‘4.0.4’ is currently being used….

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Bioconductor – mirTarRnaSeq

DOI: 10.18129/B9.bioc.mirTarRnaSeq     mirTarRnaSeq Bioconductor version: Release (3.14) mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis…

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Bioconductor – BSgenome.Ppaniscus.UCSC.panPan1

DOI: 10.18129/B9.bioc.BSgenome.Ppaniscus.UCSC.panPan1     Full genome sequences for Pan paniscus (UCSC version panPan1) Bioconductor version: Release (3.14) Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan1, May 2012) and stored in Biostrings objects. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from…

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A genome-scale screen for synthetic drivers of T cell proliferation

Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar  Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…

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Bioconductor – BSgenome.Amellifera.NCBI.AmelHAv3.1

DOI: 10.18129/B9.bioc.BSgenome.Amellifera.NCBI.AmelHAv3.1     Full genome sequences for Apis mellifera (Amel_HAv3.1) Bioconductor version: Release (3.14) Full genome sequences for Apis mellifera as provided by NCBI (assembly Amel_HAv3.1, assembly accession GCF_003254395.2) and stored in Biostrings objects. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within…

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A single-cell atlas of human and mouse white adipose tissue

Rosen, E. D. & Spiegelman, B. M. What we talk about when we talk about fat. Cell 156, 20–44 (2014). CAS  PubMed  PubMed Central  Google Scholar  Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006)….

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Bioconductor Package Installation

When I try to install the gtf for hg38 BiocManager::install(“TxDb.Hsapiens.UCSC.hg38.knownGene”) I get the following error: ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ Error in readRDS(dest) : error reading from connection Per stackoverflow.com/questions/67455984/getoptionrepos-replaces-bioconductor-standard-repositories-see-reposito I…

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Nominations for Bioconductor 2022 Awards!

News:Nominations for Bioconductor 2022 Awards! 0 @lshep Last seen 20 minutes ago United States Bioconductor is excited to announce an opportunity to recognize those making significant outstanding contributions to the Bioconductor community. The Bioconductor project is announcing the call for Bioconductor Awards, honoring various forms of contributions to the project….

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Bioconductor – cytoKernel

DOI: 10.18129/B9.bioc.cytoKernel     Differential expression using kernel-based score test Bioconductor version: Release (3.14) cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression…

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Bioconductor – sccomp (development version)

DOI: 10.18129/B9.bioc.sccomp     This is the development version of sccomp; to use it, please install the devel version of Bioconductor. Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data Bioconductor version: Development (3.15) A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model…

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Bioconductor – BSgenome.Creinhardtii.JGI.v5.6

DOI: 10.18129/B9.bioc.BSgenome.Creinhardtii.JGI.v5.6     Full genome sequences for Chlamydomonas reinhardtii (v5.6) Bioconductor version: Release (3.14) Full genome sequences for Chlamydomonas reinhardtii (v5.6) as provided by JGI and stored in Biostrings objects. The data in this package is public. See ‘citation(“BSgenome.Creinhardtii.JGI.v5.6”)’ for how to cite in publications. Author: The Bioconductor Dev…

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OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)

The organism package org.Hs.eg.db is updated twice a year in March and September, a week or two before each Bioconductor release. The current version of Org.Hs.eg.db is dated 15 September 2021. org.Hs.eg.db is 100% comprehensive in that it contains all Entrez IDs that exist at the time it is created….

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Multiple platform build/check report for BioC 3.15

Multiple platform build/check report for BioC 3.15 – BUILD results for netprioR on palomino3 This page was generated on 2022-03-03 11:10:23 -0500 (Thu, 03 Mar 2022). Hostname OS Arch (*) R version Installed pkgs nebbiolo1 Linux (Ubuntu 20.04.4 LTS) x86_64 R Under development (unstable) (2022-02-17 r81757) — “Unsuffered Consequences” 4332 riesling1 Windows Server 2019 Standard x64 R Under development (unstable) (2021-11-21 r81221) — “Unsuffered Consequences” 4093 palomino3 Windows Server 2022 Datacenter x64 R Under development (unstable) (2022-02-17 r81757 ucrt) — “Unsuffered Consequences” 4068 merida1 macOS 10.14.6 Mojave x86_64 R Under development (unstable) (2022-01-05 r81451) — “Unsuffered Consequences”…

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CHECK report for GGBase on malbec1

BioC 3.4: CHECK report for GGBase on malbec1 This page was generated on 2017-04-15 16:09:39 -0400 (Sat, 15 Apr 2017). GGBase 3.36.0VJ Carey Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) URL: hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GGBase Last Changed Rev: 122710 / Revision: 128728 Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) malbec1  Linux (Ubuntu 16.04.1 LTS) / x86_64   OK   OK  [ WARNINGS ] tokay1  Windows Server 2012 R2 Standard / x64   OK   OK   WARNINGS   OK  morelia  Mac OS X Mavericks (10.9.5) / x86_64   OK   OK   WARNINGS   OK  Summary Package: GGBase Version: 3.36.0…

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Bioconductor – GeuvadisTranscriptExpr

DOI: 10.18129/B9.bioc.GeuvadisTranscriptExpr     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GeuvadisTranscriptExpr. Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Bioconductor version: 3.8 Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from…

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Highlight points on a plot

R: Highlight points on a plot maText {marray} R Documentation Highlight points on a plot Description This function may be used to highlight a subset of points on an existing plot, such as a plot produced by plot, maPlot, or maPlot.func. Usage maText(subset=NULL, labels=as.character(1:length(subset)), …) Arguments subset A “logical” or…

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Identification of Hub Genes Associated with COPD Through Integrated Bi

Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…

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Bioconductor – TAPseq

DOI: 10.18129/B9.bioc.TAPseq     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TAPseq. Targeted scRNA-seq primer design for TAP-seq Bioconductor version: 3.12 Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using…

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Bioconductor – branchpointer

DOI: 10.18129/B9.bioc.branchpointer     Prediction of intronic splicing branchpoints Bioconductor version: Release (3.14) Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs. Author: Beth Signal Maintainer: Beth Signal <b.signal at garvan.org.au> Citation (from within R,…

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Validation of hub genes in acute pancreatitis

Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…

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r – Contrast for Limma – Voom

I’m doing a differential expression analysis for RNA-seq data with limma – voom. My data is about a cancer drug, 49 samples in total, some of them are responders some of them are not. I need some help building the contrast. I’m dealing with only one factor here, so two…

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nf-core/circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data Introduction nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across…

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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 – adaptest

DOI: 10.18129/B9.bioc.adaptest     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see adaptest. Data-Adaptive Statistics for High-Dimensional Multiple Testing Bioconductor version: 3.11 Data-adaptive test statistics represent a general methodology for performing multiple hypothesis testing on effects sizes while maintaining honest statistical inference when…

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Bioconductor – OGRE (development version)

DOI: 10.18129/B9.bioc.OGRE     This is the development version of OGRE; to use it, please install the devel version of Bioconductor. Calculate, visualize and analyse overlap between genomic regions Bioconductor version: Development (3.15) OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs,…

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Fatty infiltration after rotator cuff tear

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

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use tcgabiolinks package to download TCGA data

TCGA Data download in terms of ease of use ,RTCGA The bag should be better , And because it’s already downloaded data , The use is relatively stable . But also because of the downloaded data , There is no guarantee that the data is new .TCGAbiolinks The package is…

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Bioconductor – txcutr (development version)

DOI: 10.18129/B9.bioc.txcutr     This is the development version of txcutr; for the stable release version, see txcutr. Transcriptome CUTteR Bioconductor version: Development (3.15) Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can…

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Bioconductor – r3Cseq

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see r3Cseq. Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq) Bioconductor version: 3.3 This package is an implementation of data analysis for the long-range interactions from 3C-seq assay. Author: Supat Thongjuea, MRC Molecular…

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Bioconductor – EGSEA123

DOI: 10.18129/B9.bioc.EGSEA123     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see EGSEA123. Easy and efficient ensemble gene set testing with EGSEA Bioconductor version: 3.13 R package that supports the F1000Research workflow article `Easy and efficient ensemble gene set testing with EGSEA’, Alhamdoosh…

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Bioconductor – BSgenome.Scerevisiae.UCSC.sacCer3

DOI: 10.18129/B9.bioc.BSgenome.Scerevisiae.UCSC.sacCer3     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Scerevisiae.UCSC.sacCer3. Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer3) Bioconductor version: 3.10 Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer3, April 2011) and stored in Biostrings objects. Author: The…

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Bioconductor – pRolocGUI

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see pRolocGUI. Interactive visualisation of spatial proteomics data Bioconductor version: 3.4 The package pRolocGUI comprises functions to interactively visualise organelle (spatial) proteomics data on the basis of pRoloc, pRolocdata and shiny. Author: Lisa M…

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[BioC] DESeq2, plotting residuals vs.fitted values

On the scale of the counts, the fitted values are: assays(dds)[[“mu”]] to get the fitted values on the common scale, you just need to divideeach column by the size factor: fitted.common.scale = t( t( assays(dds)[[“mu”]] ) / sizeFactors(dds) ) So then the residuals are counts(dds, normalized=TRUE) – fitted.common.scale Dear All,I…

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Bioconductor – AHLRBaseDbs

DOI: 10.18129/B9.bioc.AHLRBaseDbs     LRBaseDbs for AnnotationHub Bioconductor version: Release (3.14) Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the README.md of lrbase-workflow. Author: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido…

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Spatial components of molecular tissue biology

1. Okabe, Y. & Medzhitov, R. Tissue biology perspective on macrophages. Nat. Immunol. 17, 9–17 (2016). CAS PubMed  Google Scholar  2. Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl Acad. Sci. USA…

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Bioconductor – DaMiRseq (development version)

DOI: 10.18129/B9.bioc.DaMiRseq     This is the development version of DaMiRseq; for the stable release version, see DaMiRseq. Data Mining for RNA-seq data: normalization, feature selection and classification Bioconductor version: Development (3.15) The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them…

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bioconductor – Trouble installing Rhtslib in R/R studio

I’m using RStudio on Ubuntu 18 and I’m trying to install the htslib package from the Bioconductor repo, but I’m stuck now. This is what I get: * installing *source* package ‘Rhtslib’ … ** using non-staged installation via StagedInstall field ** libs cd “htslib-1.7” && make -f “/usr/lib/R/etc/Makeconf” -f “Makefile.Rhtslib”…

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Bioconductor on Microsoft Azure – Microsoft Tech Community

Co-authored by: Nitesh Turaga – Scientist at Dana Farber/Harvard, Bioconductor Core Team Erdal Cosgun – Sr. Data Scientist at Microsoft Biomedical Platforms and Genomics team Vincent Carey – Professor at Harvard Medical School, Bioconductor Core Team   Introduction   The Bioconductor project promotes the statistical analysis and comprehension of current and emerging…

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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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Novel diagnostic biomarkers for keloid based on GEO database

Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…

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Bioconductor – cleaver

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see cleaver. Cleavage of polypeptide sequences Bioconductor version: 2.13 In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: web.expasy.org/peptide_cutter/peptidecutter_enzymes.html Author: Sebastian Gibb [aut, cre] Maintainer: Sebastian Gibb <mail at sebastiangibb.de> Citation (from…

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CRAN Package Depends on Bioconductor Package Installing error

In R 3.0.2, the following works: At the time of this writing, the value ind can take a vector with values between 1 and 8, and the following meaning: 1: CRAN 2: BioC software 3: BioC annotation 4: BioC experiment 5: BioC extra 6: Omegahat 7: R-Forge 8: rforge.net This…

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Introduction to RNA-seq data analysis – Extended Materials

Introduction to RNA-seq data analysis – Extended Materials | cruk-summer-school-2021 Github repo for 2021 CRUK-CC Bioinformatics Summer School (tinyurl.com/crukss2021) Taught remotely Bioinformatics Training, Craik-Marshall Building, Downing Site, University of Cambridge Supplementary materials These files contain some additional information and exercises not included during the taught course. Obtaining public data Raw…

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[BioC] removal of affymetrix control probes from ExpressionSet

Hi Brian, library(genefilter)filtered<-featureFilter(eset, require.entrez=F, remove.dupEntrez=F) Cheers,Yuan Hi,What’s the easiest way, given an ExpressionSet object, to remove just thecontrol probes (i.e. those that start with AFFX-….)?Thanks!Brian.[[alternative HTML version deleted]]_______________________________________________Bioconductor mailing listBioconductor at r-project.orgstat.ethz.ch/mailman/listinfo/bioconductornews.gmane.org/gmane.science.biology.informatics.conductor Read more here: Source link

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Installing Bioconductor packages error –> Error in readRDS(dest) : error reading from connection

I have been trying to install Bioconductor in R (version 4.0.5). Each time I try to insert the following code, I get some error like: >if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(version = “3.12”) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.csiro.au/ Bioconductor version 3.12…

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Cannot install Phyloseq and dada2

Hello all, I have been having issues installing packages that I really need to use. Basically, I cannot download either Phyloseq or dada2 and I believe it’s because I don’t have GenomeInfoDbData. But at the same time, I cannot install GenomeInfoDbData because I can’t seem to update the dependencies (“fansi”…

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traviz 1.0.0 installation fails: ERROR: lazy loading failed

Hi, I cannot install traviz package (version 1.0.0) from Bioconductor on a linux machine (from source). I have a conda environment, and I installed traviz from conda, but it cannot be used – when I do library(traviz) R just crashes and quits without any message. So I tried to install…

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Bioconductor – mirbase.db

DOI: 10.18129/B9.bioc.mirbase.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see mirbase.db. miRBase: the microRNA database Bioconductor version: 3.11 miRBase: the microRNA database assembled using data from miRBase (www.mirbase.org/). Author: James F. Reid <reidjf at gmail.com> Maintainer: James F. Reid <reidjf at…

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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 – GSE13015

DOI: 10.18129/B9.bioc.GSE13015     GEO accession data GSE13015_GPL6106 as a SummarizedExperiment Bioconductor version: Release (3.14) Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data…

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Bioconductor – RiboCrypt

DOI: 10.18129/B9.bioc.RiboCrypt     Interactive visualization in genomics Bioconductor version: Release (3.14) R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots….

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Bioconductor – chromhmmData

DOI: 10.18129/B9.bioc.chromhmmData     Chromosome Size, Coordinates and Anchor Files Bioconductor version: Release (3.14) Annotation files of the formatted genomic annotation for ChromHMM. Three types of text files are included the chromosome sizes, region coordinates and anchors specifying the transcription start and end sites. The package includes data for two…

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Identification of differentially expressed genes in AF

Defeng Pan,1,&ast; Yufei Zhou,2,&ast; Shengjue Xiao,1,&ast; Yue Hu,3,&ast; Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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Bioconductor – derfinder (development version)

DOI: 10.18129/B9.bioc.derfinder     This is the development version of derfinder; for the stable release version, see derfinder. Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach Bioconductor version: Development (3.15) This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two…

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Bioconductor – RDAVIDWebService

DOI: 10.18129/B9.bioc.RDAVIDWebService     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RDAVIDWebService. An R Package for retrieving data from DAVID into R objects using Web Services API. Bioconductor version: 3.12 Tools for retrieving data from the Database for Annotation, Visualization and Integrated…

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Bioconductor – vbmp

DOI: 10.18129/B9.bioc.vbmp     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see vbmp. Variational Bayesian Multinomial Probit Regression Bioconductor version: 3.12 Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the…

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Bioconductor – rTRMui (development version)

DOI: 10.18129/B9.bioc.rTRMui     This is the development version of rTRMui; for the stable release version, see rTRMui. A shiny user interface for rTRM Bioconductor version: Development (3.15) This package provides a web interface to compute transcriptional regulatory modules with rTRM. Author: Diego Diez Maintainer: Diego Diez <diego10ruiz at gmail.com>…

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Bioconductor – TBSignatureProfiler (development version)

DOI: 10.18129/B9.bioc.TBSignatureProfiler     This is the development version of TBSignatureProfiler; for the stable release version, see TBSignatureProfiler. Profile RNA-Seq Data Using TB Pathway Signatures Bioconductor version: Development (3.15) Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates…

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Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

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Bioconductor – bnem (development version)

DOI: 10.18129/B9.bioc.bnem     This is the development version of bnem; for the stable release version, see bnem. Training of logical models from indirect measurements of perturbation experiments Bioconductor version: Development (3.15) bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of…

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Expressionset – phenodata – Stackify

The correct place for this question is on the Bioconductor support site. It’s better to provide a reproducible example that captures the essence of the problem; creating the reproducible example often helps to identify the reason for the problem. library(Biobase) exprs <- matrix(0, nrow=5, ncol=3, dimnames=list(letters[1:5], LETTERS[1:3])) pData <- data.frame(id=c(“foo”,…

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Bioconductor – ChIPQC

    This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see ChIPQC. Quality metrics for ChIPseq data Bioconductor version: 3.1 Quality metrics for ChIPseq data Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Rory Stark <rory.stark…

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Bioconductor – easierData

DOI: 10.18129/B9.bioc.easierData     easier internal data and exemplary dataset from IMvigor210CoreBiologies package Bioconductor version: Release (3.14) Access to internal data required for the functional performance of easier package and exemplary bladder cancer dataset with both processed RNA-seq data and information on response to ICB therapy generated by Mariathasan et…

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GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

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Valine tRNA levels and availability regulate complex I assembly in leukaemia

1. Rapino, F. et al. Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature 558, 605–609 (2018). CAS  PubMed  Google Scholar  2. Goodarzi, H. et al. Modulated expression of specific tRNAs drives gene expression and cancer progression. Cell 165, 1416–1427 (2016). CAS  PubMed  PubMed Central  Google Scholar  3. Wolfe, A….

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Principal Scientist, Disease Strategy (Translational bioinformatics) on beHired.in

At Bristol Myers Squibb, we are inspired by a single vision – transforming patients’ lives through science. In oncology, hematology, immunology and cardiovascular disease – and one of the most diverse and promising pipelines in the industry – each of our passionate colleagues contribute to innovations that drive meaningful change. We…

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Bioconductor – monaLisa

DOI: 10.18129/B9.bioc.monaLisa     Binned Motif Enrichment Analysis and Visualization Bioconductor version: Release (3.14) Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility…

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Bioconductor – BSgenome.Hsapiens.NCBI.GRCh38

DOI: 10.18129/B9.bioc.BSgenome.Hsapiens.NCBI.GRCh38     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Hsapiens.NCBI.GRCh38. Full genome sequences for Homo sapiens (GRCh38) Bioconductor version: 3.11 Full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects. Author: The…

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Bioconductor – ProteoDisco

DOI: 10.18129/B9.bioc.ProteoDisco     Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Release (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript…

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Bioconductor – BSgenome.Mmulatta.UCSC.rheMac10

DOI: 10.18129/B9.bioc.BSgenome.Mmulatta.UCSC.rheMac10     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Mmulatta.UCSC.rheMac10. Full genome sequences for Macaca mulatta (UCSC version rheMac10) Bioconductor version: 3.11 Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac10, Feb. 2019) and stored in Biostrings…

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Bioinformatics Core Facility staff position at IMB in Mainz, Germany

www.imb.de/jobs/jobdetail/bioinformatician Bioinformatician (m/f/d) (#CFBIO17) IMB (www.imb.de) is a research centre on the campus of Mainz University, Germany. It is generously funded by the Boehringer Ingelheim Foundation and the state of Rhineland-Palatinate. Our research focuses on the biology of the cell nucleus and ranges from the molecular level to organismic, systems…

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Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells | BMC Genomics

1. Yin H, Price F, Rudnicki MA. Satellite cells and the muscle stem cell niche. Physiol Rev. 2013;93(1):23–67. CAS  PubMed  PubMed Central  Google Scholar  2. Hoppeler H, Fluck M. Plasticity of skeletal muscle mitochondria: structure and function. Med Sci Sport Exer. 2003;35(1):95–104. CAS  Google Scholar  3. Astruc T: Carcass Composition,…

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Bioconductor Tools for Microarray Data Analysis

References ………………………………………………………………………………………..478 17.1 INTRODUCTION 17.1.1 WHAT IS BIOCONDUCTOR? Bioconductor [1] is an open source software project for the R statistical computing language. The main aim of the project is to provide R packages to facilitate the analysis of DNA microarray, sequencing, SNP and other genomic data. In addition for data,…

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conversion of ensembl to gene_symbol in seurat

I am working on spatial 10X visum data. Space ranger was used for the identification of filtered_feature_bc_matrix.h5 matrix and given as input in Seurat R package. For Quality filteration, I would like to have gene symbol but my features consist of ENSEMBL ids. How can I change the ENSEMBL to…

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