Tag: Bioconductor

Bioconductor – SNPlocs.Hsapiens.dbSNP155.GRCh37 (development version)

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP155.GRCh37     This is the development version of SNPlocs.Hsapiens.dbSNP155.GRCh37; to use it, please install the devel version of Bioconductor. Human SNP locations and alleles extracted from dbSNP Build 155 and placed on the GRCh37/hg19 assembly Bioconductor version: Development (3.16) The 929,496,192 SNPs in this package were extracted from…

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DE analysis with multiple factors

DE analysis with multiple factors 0 Hi all, I’m using DEP R package to perform analysis (including DE analysis) on proteins across different conditions bioconductor.org/packages/devel/bioc/vignettes/DEP/inst/doc/DEP.html The package uses limma for DE analysis My experiment is structured as : sample – disease_state( disease / healthy) – environment (env1 / env2) I…

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The crisprVerse: a comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies

Abstract The success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods for advanced…

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[Internship] Bioinformatics Intern, Fall 2022 at Harmonic Discovery (United States)

About Us Based in NYC, Harmonic Discovery is a biotechnology company leveraging biology, medicinal chemistry, and machine learning to create a new generation of therapeutics for oncology and autoimmune disorders. We look for passionate innovators, radical thinkers, and collaborative builders. It’s time to integrate our understanding of biology and chemistry…

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r – How can I install the Bioconductor package “liftOver” in a conda environment?

I’m trying to install the Bioconductor package liftOver using conda. I’m creating a conda environment using a .yml file like this: conda env create -f coo_environment.yml When I do this, I get: Collecting package metadata: done Solving environment: failed ResolvePackageNotFound: – bioconductor-liftover The relevant contents of coo_environment.yml are shown below…

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Bioconductor – lumi

DOI: 10.18129/B9.bioc.lumi     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see lumi. BeadArray Specific Methods for Illumina Methylation and Expression Microarrays Bioconductor version: 3.12 The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina…

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Acute phase of ischemia-reperfusion in rats

Introduction Stroke is one of the leading causes of death and disability worldwide, which causes substantial economic and social burdens.1 Ischemic stroke is caused by insufficient blood and oxygen supply to the brain,2 accounting for about 85% of the casualties of stroke patients.3 The concept of treatment for ischemic injury…

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Bioconductor – mvoutData (development version)

DOI: 10.18129/B9.bioc.mvoutData     This is the development version of mvoutData; for the stable release version, see mvoutData. affy and illumina raw data for assessing outlier detector performance Bioconductor version: Development (3.16) affy and illumina raw data for assessing outlier detector performance Author: VJ Carey <stvjc at channing.harvard.edu> Maintainer: VJ…

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I cannot install “microbiome”

Hi there, i cannot install package “microbiome” in R (ver 4.2.1), when i input the code, it seems OK, BiocManager::install(“microbiome”, force = TRUE) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt) Installing package(s) ‘microbiome’ trying URL…

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Bioconductor – cqn (development version)

DOI: 10.18129/B9.bioc.cqn     This is the development version of cqn; for the stable release version, see cqn. Conditional quantile normalization Bioconductor version: Development (3.16) A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. Author: Jean (Zhijin) Wu, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen <kasperdanielhansen at…

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Bioconductor – BSgenome.Gmax.NCBI.Gmv40

DOI: 10.18129/B9.bioc.BSgenome.Gmax.NCBI.Gmv40     Full genome sequences for Glycine max (Gmv40) Bioconductor version: Release (3.15) Full genome sequences for Glycine max as provided by NCBI (assembly Glycine_max_v4.0, assembly accession GCF_000004515.5) and stored in Biostrings objects. Author: Deisiany Ferreira Neres <deisianyufg at gmail.com> Maintainer: Deisiany Ferreira Neres <deisianyufg at gmail.com>, Clay…

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I have a query regarding differential gene expression using limma-voom.

I have a query regarding differential gene expression using limma-voom. 1 @28946033 Last seen 1 day ago India I used the following pipeline for RNA Seq Analysis Fastq-Trimmomatic- Hisat2(gtf file was annotated)-featurecounts After featurecounts I tried to do limmavoom, but I get error saying this An error occurred with this…

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Computational Biologist, Clinical Bioinformatics – Remote job in Boston, Massachusetts at Dana-Farber Cancer Institute

Computational Biologist, Clinical Bioinformatics – Remote Job Details Job ID: 26821 Location: 450 Brookline Ave, Boston, MA 02215 Category: Clinical Research Employment Type: Full time Work Location: Full Remote: 4-5 days remote/wk Overview The NGS Bioinformatics Group at Dana-Farber Cancer Institute seeks a Computational Biologist to work on Profile, our…

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Director, Bioinformatics Core at BIDMC

Department Description: About us: The BIDMC Bioinformatics Core (BBC) is part of the Precision RNA Medicine Core at Beth Israel Lahey Health. The BBC will be tightly integrated with the ‘Omics cores at BIDMC. It is the center for bioinformatics research expertise at BIDMC. We work directly with biomedical scientists…

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Bioconductor – fmrs

DOI: 10.18129/B9.bioc.fmrs     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see fmrs. Variable Selection in Finite Mixture of AFT Regression and FMR Bioconductor version: 3.13 Provides parameter estimation as well as variable selection in Finite Mixture of Accelerated Failure Time Regression and…

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Alternatives and detailed information of monocle3

Licence: other No description or website provided. Projects that are alternatives of or similar to monocle3 dropEst Pipeline for initial analysis of droplet-based single-cell RNA-seq data Stars: ✭ 71 (-58.24%) Mutual labels:  single-cell-rna-seq StackedDAE Stacked Denoising AutoEncoder based on TensorFlow Stars: ✭ 23 (-86.47%) Mutual labels:  single-cell-rna-seq kmer-homology-paper Manuscript for functional prediction…

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bioconductor – Generating graphical results within from bioinformatics/nature genomics papers

I am a computational scientist with background in computer science and engineering however very new to the field of bioinformatics and computational genomics. Looking at papers in nature, PLOS, Cell, PNAS etc. within the topic of computational genomics, I see a very similar set of very sophisticated graphical results, ranging…

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Sr. Bioinformatics-Clinical Database Developer – CBL Path, Inc

Job Functions, Duties, Responsibilities and Position Qualifications: POSITION TITLE:Senior Bioinformatics-Clinical Database Developer STANDARDIZED JOB TITLE: Database Development, Web Application Development, and Clinical Analytics EXEMPT STATUS:  Exempt POSITION SUMMARY: Sr. Database Developer works with cross-functional groups & Medical Leadership for developing a databases for a clinical assays. The candidate is expected…

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Senior Scientist Applied Bioinformatics Job In San Francisco, CA 94103| TechCareers

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….

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Bioconductor – HPiP

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

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Bioconductor – BSgenome.Btaurus.UCSC.bosTau9.masked (development version)

DOI: 10.18129/B9.bioc.BSgenome.Btaurus.UCSC.bosTau9.masked     This is the development version of BSgenome.Btaurus.UCSC.bosTau9.masked; for the stable release version, see BSgenome.Btaurus.UCSC.bosTau9.masked. Full masked genome sequences for Bos taurus (UCSC version bosTau9) Bioconductor version: Development (3.16) Full genome sequences for Bos taurus (Cow) as provided by UCSC (genome bosTau9) and stored in Biostrings objects….

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Bioconductor – TrajectoryGeometry (development version)

DOI: 10.18129/B9.bioc.TrajectoryGeometry     This is the development version of TrajectoryGeometry; for the stable release version, see TrajectoryGeometry. This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns Bioconductor version: Development (3.16) Given a time series or pseudo-times series of gene expression data, we might wish to…

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Postdoctoral position in Bioinformatics at Uppsala, Sweden, Aug 2022

The postdoctoral fellow position in Bioinformatics is available for applicants with a doctoral degree at the Department of Cell and Molecular Biology, Uppsala University, Sweden, in August 2022. General Info Position: Postdoctoral FellowNo. of Positions: 1Research Field: Bioinformatics, Computational BiologyJoining Date: ASAPContract Period: 2 YearsSalary: Subject to norms Workplace: Department…

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rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses | BMC Bioinformatics

Case study To illustrate and evaluate the functionality of rprimer, two assays targeted at norovirus GI were designed. Assay A: RT-qPCR for quantitative detection of norovirus GI The first task was to design a broadly reactive RT-qPCR assay for quantitative detection. For this, we decided to use the ‘ambiguous’ primer…

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Bioconductor – interacCircos (development version)

DOI: 10.18129/B9.bioc.interacCircos     This is the development version of interacCircos; for the stable release version, see interacCircos. The Generation of Interactive Circos Plot Bioconductor version: Development (3.16) Implement in an efficient approach to display the genomic data, relationship, information in an interactive circular genome(Circos) plot. ‘interacCircos’ are inspired by…

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SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma

Clapier, C. R., Iwasa, J., Cairns, B. R. & Peterson, C. L. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat. Rev. Mol. Cell Biol. 18, 407–422 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes….

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Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

Subjects Normal breast and tumor samples were obtained with the written informed consent from donors and appropriate approval from local ethical committees, with the detailed information described in the respective original publications: normal tissue9, METABRIC14, TCGA35. Differential allelic expression analysis DNA and total RNA from 64 samples of normal breast…

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Bioconductor – sSNAPPY (development version)

DOI: 10.18129/B9.bioc.sSNAPPY     This is the development version of sSNAPPY; for the stable release version, see sSNAPPY. Single Sample directioNAl Pathway Perturbation analYsis Bioconductor version: Development (3.16) A single sample pathway pertrubation testing methods for RNA-seq data. The method propagate changes in gene expression down gene-set topologies to compute…

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Bioconductor – BSgenome.Cjacchus.UCSC.calJac4

DOI: 10.18129/B9.bioc.BSgenome.Cjacchus.UCSC.calJac4     Full genome sequences for Callithrix jacchus (UCSC version calJac4) Bioconductor version: Release (3.15) Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac4, May 2020) and wrapped in a BSgenome object. Author: The Bioconductor Dev Team Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation…

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Bioconductor – ComplexHeatmap

DOI: 10.18129/B9.bioc.ComplexHeatmap     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ComplexHeatmap. Make Complex Heatmaps Bioconductor version: 3.14 Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly…

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Deseq2 Multifactor Design – Design Forum

Deseq2 multifactor design – In fact, deseq2 can analyze any possible experimental design that can be expressed with fixed effects terms (multiple factors, designs with interactions, designs with continuous variables, splines, and so on are all possible). We have searched different posts in different forums and i can’t figure out…

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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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