Tag: Bioconductor

R/Bioconductor for Mass Spectrometry and Proteomics

News:Course – R/Bioconductor for Mass Spectrometry and Proteomics 0 Course: R/Bioconductor for Mass Spectrometry and Proteomics Format: Online, 27-29 March 2023 Overview This course will introduce participants to the analysis and exploration of mass spectrometry (MS) based proteomics data using R and Bioconductor. The course will cover all levels of…

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Are we tricking ourselves with batch effect correction?

Hi Christian I found your post a little late, but I found it so interesting that a will give it a late answer. In your description of your experiment, you do not inform of the experiment design, if the batches contained the same proportion of samples from your biological groups….

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Statistical Approach to Study Microarray Analysis Using Bioconductor Study of gene expression using, ISBN: 9783659133411, 3659133418

Store  Condition  Coupons & Deals  Price  Shipping  Total  Chegg Semester Rental (Due Date 05/27/2023) Semester Rental (Due Date 05/27/2023) $40.99as of 1 second ago $4.99 Abebooks(Marketplace) New New $62.99as of 1 second ago FREE Amazon(Marketplace) New New $ Amazon coupon(s) Details: Get FREE Shipping with a $25+ purchase Restrictions: Spend…

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Bioconductor – MEDIPS

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see MEDIPS. DNA IP-seq data analysis Bioconductor version: 3.2 MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of…

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Bioconductor – hgu95bcdf

DOI: 10.18129/B9.bioc.hgu95bcdf     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see hgu95bcdf. hgu95bcdf Bioconductor version: 3.10 A package containing an environment representing the HG_U95B.CDF file. Author: The Bioconductor Project Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“hgu95bcdf”)):…

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Bioinformatics Scientist (Statistical Programming/Data Manipulation) – Rangam Consultants Inc.

Hybrid role Research Scientist, Early Development Predictive Sciences We are seeking an innovative scientist to join our Informatics Predictive Sciences team. Roles and responsibilities: Performing computational biology analysis for exploration and interpretation of omic datasets, including bulk and single-cell RNASeq, DNA methylation, Exome/Genome sequencing, cytokine, and proteomic data. Integrative analysis…

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How to translate CDS to an amino acid sequence

How to translate CDS to an amino acid sequence 2 How to translate CDS to amino acid sequence? This site shows CDS and translations but no explanation on how to get there. translation CDS sequencing • 1.3k views • link updated 2 hours ago by vvasta • 0 • written…

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Bioconductor – RTCGA.clinical

DOI: 10.18129/B9.bioc.RTCGA.clinical     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see RTCGA.clinical. Clinical datasets from The Cancer Genome Atlas Project Bioconductor version: 3.8 Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from gdac.broadinstitute.org/. Clinical data format…

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Bioconductor – GMRP

DOI: 10.18129/B9.bioc.GMRP     GWAS-based Mendelian Randomization and Path Analyses Bioconductor version: Release (3.11) Perform Mendelian randomization analysis of multiple SNPs to determine risk factors causing disease of study and to exclude confounding variabels and perform path analysis to construct path of risk factors to the disease. Author: Yuan-De Tan…

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CTCF: an R/bioconductor data package of human and mouse CTCF binding sites

. 2022 Dec 16;2(1):vbac097. doi: 10.1093/bioadv/vbac097. eCollection 2022. Affiliations Expand Affiliations 1 Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA. 2 Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA. 3 Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA. 4 Curriculum in…

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Alternatives to perform peptide identification in Bioconductor version ‘3.16’?

Alternatives to perform peptide identification in Bioconductor version ‘3.16’? 0 @23d16096 Last seen 4 hours ago United States MSGFplus and rTANDEM are both deprecated in Bioconductor version ‘3.16’. Are there any alternatives to perform peptide identification with spectral libraries? Code should be placed in three backticks as shown below #…

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Scientist II, Bioinformatics Job Opening in South Plainfield, NJ at PTC Therapeutics, Inc.

Job Posting for Scientist II, Bioinformatics at PTC Therapeutics, Inc. Job Description Summary: The Scientist II, Bioinformatics is responsible for planning and performing scientific experiments that contribute to PTC’s research and drug discovery activities. The Scientist II is also responsible for communicating experimental results to his/her supervisor and…

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Whole-transcriptome profiling across different developmental stages of Aedes albopictus (Diptera: Culicidae) provides insights into chitin-related non-coding RNA and competing endogenous RNA networks | Parasites & Vectors

Benelli G, Wilke A, Beier JC. Aedes albopictus (Asian Tiger Mosquito). Trends Parasitol. 2020;36:942–3. Article  Google Scholar  Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nature. 2013;496:504–7. Article  CAS  Google Scholar  Bonizzoni M, Gasperi G, Chen X,…

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I cannot install annotables package in Rstudio (macOS)

I cannot install annotables package in Rstudio (macOS) 1 @4f002f4c Last seen 1 hour ago Canada I cannot install annotables on Rstudio. I have tried updating R to 4.2.2, it did not work on 4.2.1 or the new version. I was able to install BiocManager and several BiocManager packages using…

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Annelid functional genomics reveal the origins of bilaterian life cycles

Hall, B. K. & Wake, M. H. in The Origin and Evolution of Larval Forms (eds Hall, B. K. & Wake, M. H.) 1–19 (Academic Press, 1999). Nielsen, C. Animal phylogeny in the light of the trochaea theory. Biol. J. Linn. Soc. 25, 243–299 (2008). Article  Google Scholar  Garstang, W….

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Seeking members for BioC2023 organizing committee

News:Seeking members for BioC2023 organizing committee 0 @mariadoyle-23960 Last seen 19 minutes ago Ireland The organizing committee for the 2023 Bioconductor conference (BioC2023), to be held in Boston August 2-4, is looking for organizers to help in planning the event. Participation involves attending approximately monthly remote meetings (more frequently as…

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Bioconductor – IntOMICS (development version)

DOI: 10.18129/B9.bioc.IntOMICS     This is the development version of IntOMICS; to use it, please install the devel version of Bioconductor. Integrative analysis of multi-omics data to infer regulatory networks Bioconductor version: Development (3.17) IntOMICS is an efficient integrative framework based on Bayesian networks. IntOMICS systematically analyses gene expression (GE),…

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Bioconductor drawProteins alternative in Python

Bioconductor drawProteins alternative in Python 0 Is there an equivalent package or library in Python to represent protein with its domains and motif, like in the image below? I searched for it, but most python libraries focus on 3D representations rather than a more schematical one. This image was generated…

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limma issue (possibly a Galaxy issue)

limma issue (possibly a Galaxy issue) 0 I just wanted to alert the community to an issue I discovered while using limma on the Galaxy webserver. The issue arises when conducting differential expression between contrasts. The process is described on the galaxy server as follows: “Names of two groups to…

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How to select data from assays list in SummarizedExperiment to plot

How to select data from assays list in SummarizedExperiment to plot 0 I am using DEP Bioconductor package bioconductor.org/packages/release/bioc/vignettes/DEP/inst/doc/DEP.html I want to visualize normal distribution of data using fitdistrplus pakage’s descdist function However I get an error. How can I select data from assays list in SummarizedExperiment to plot? data_norm…

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Bioconductor – optimalFlow (development version)

DOI: 10.18129/B9.bioc.optimalFlow     This is the development version of optimalFlow; for the stable release version, see optimalFlow. optimalFlow Bioconductor version: Development (3.17) Optimal-transport techniques applied to supervised flow cytometry gating. Author: Hristo Inouzhe <hristo.inouzhe at gmail.com> Maintainer: Hristo Inouzhe <hristo.inouzhe at gmail.com> Citation (from within R, enter citation(“optimalFlow”)): Installation…

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ValueError: unsupported format character ‘T’ (0x54) at index 3312 when creating environment from environment file – Technical Support

Here’s my command:conda env create -n test-qiime2_env -f qiime2-2022.11-py38-linux-conda.yml 2> qiime2-2022.11-py38-linux-conda.yml.e 1> qiime2-2022.11-py38-linux-conda.yml.o Here’s my log files: (base) cat qiime2-2022.11-py38-linux-conda.yml.o Collecting package metadata (repodata.json): …working… done Solving environment: …working… done Preparing transaction: …working… done Verifying transaction: …working… done Executing transaction: …working… done Rolling back transaction: …working… done (base) cat qiime2-2022.11-py38-linux-conda.yml.e…

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Extracting DEseq2 results ?resultnames

Dear Community, I am using the DEseq2 package to analyze my time series data, and referring this vignet (master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments ) In brief, the dataset has two groups OP50 (control group) and SC20 (test group), harvested at 7 different time points. we are interested in DE genes in SC20 compared to…

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Senescent cells perturb intestinal stem cell differentiation through Ptk7 induced noncanonical Wnt and YAP signaling

Childs, B. G. et al. Senescent cells: an emerging target for diseases of ageing. Nat. Rev. Drug Discov. 16, 718–735 (2017). Article  CAS  Google Scholar  Gil, J. Cellular senescence causes ageing. Nat. Rev. Mol. Cell Biol. 20, 388 (2019). Article  CAS  Google Scholar  van Deursen, J. M. The role of…

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microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene

microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene 0 @lluis-revilla-sancho Last seen 8 hours ago European Union I was looking to some examples and I could retrieve the microRNAs of the hg19 transcriptome, but not from the hg38 transcript annotation. I realized this might be because TxDb.Hsapiens.UCSC.hg38.knownGene doesn’t have a miRBase build ID,…

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Bioconductor – MSstatsShiny

DOI: 10.18129/B9.bioc.MSstatsShiny     MSstats GUI for Statistical Anaylsis of Proteomics Experiments Bioconductor version: Release (3.16) MSstatsShiny is an R-Shiny graphical user interface (GUI) integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of experimental designs….

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an R/Bioconductor package for the inference and analysis of synteny networks

Please use this url to cite or link to this publication: hdl.handle.net/1854/LU-01GP3AHHZ8VR3BTBCPA6FEXGM0 MLA De Almeida Silva, Fabricio, Tao Zhao, Kristian K Ullrich, M Eric Schranz, and Yves Van de Peer. 2023. “Syntenet: An R/Bioconductor Package for the Inference and Analysis of Synteny Networks.” Ed by. Pier Luigi Martelli. Bioinformatics. doi:10.1093/bioinformatics/btac806….

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chromosome start & end for genes in biomart R not showing

chromosome start & end for genes in biomart R not showing 1 I have a list of genes which i want to get their cordinates and ref-seq ids but “start” & “end” attributes in biomart keeps throwing error. could you please take a look? library(biomart) #define which database to use…

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Error printing a CompressedGRangesList

I’m trying to annotate some data from a Bisulphite experiment, from which I have a GRanges object without any annotation: GRanges object with 872900 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr10 48196 * [2] chr10 48486 * [3] chr10 49247 * [4] chr10 49258…

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Bioconductor – CONSTANd (development version)

DOI: 10.18129/B9.bioc.CONSTANd     This is the development version of CONSTANd; for the stable release version, see CONSTANd. Data normalization by matrix raking Bioconductor version: Development (3.17) Normalizes a data matrix `data` by raking (using the RAS method by Bacharach, see references) the Nrows by Ncols matrix such that the…

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Bioconductor – BSgenome.Scerevisiae.UCSC.sacCer1

DOI: 10.18129/B9.bioc.BSgenome.Scerevisiae.UCSC.sacCer1     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Scerevisiae.UCSC.sacCer1. Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer1) Bioconductor version: 3.12 Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer1, Oct. 2003) and stored in Biostrings objects. Author: The…

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Bioconductor – Travel

DOI: 10.18129/B9.bioc.Travel     An utility to create an ALTREP object with a virtual pointer Bioconductor version: Release (3.16) Creates a virtual pointer for R’s ALTREP object which does not have the data allocates in memory. The pointer is made by the file mapping of a virtual file so it…

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DeSeq2 and GenomicRange installation possible conflict with bioconductor version 3.16?

Enter the body of text here I’ve tried to install DeSeq2. and received the following warnings as shown below Code should be placed in three backticks as shown below “`Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.1 (2022-06-23) Installing package(s) ‘DESeq2’ Warning: unable to access index for repository www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2: cannot open…

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Error when Installing BioConductor Package (‘affy’)

Hi, when I try to install Bioconductor package ‘affy’ Experience below error\ May I know how do I fix this? I’m currently using R4.2.2 on MacBook Air, M1\ R version 4.2.2 (2022-10-31) — “Innocent and Trusting”\ Copyright (C) 2022 The R Foundation for Statistical Computing\ Platform: aarch64-apple-darwin20 (64-bit) BiocManager::install(“affy”) ‘getOption(“repos”)’…

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query regarding error in installation of “goseq” R bioconductor package

query regarding error in installation of “goseq” R bioconductor package 0 @6d5973d2 Last seen 19 hours ago India I am trying to install “goseq” Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2 I getting many error messages which are…

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r – Cannot Install maftools into BiocManager due to RSQLite

I am a relatively new R-user. I am currently working on trying to read .maf files via the maftools package released by Bioconductor. I am following the instructions as posted on the Bioconductor website (www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html#4_Installation), however, everytime I attempt to run the installation, it gets stuck on RSQLite and I…

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Bioconductor – EasyCellType

DOI: 10.18129/B9.bioc.EasyCellType     Annotate cell types for scRNA-seq data Bioconductor version: Release (3.16) We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA)…

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lazy loading failed, unable to load shared object rtracklayer.so

Hello! I am working on analyzing a dataset I created with the 10x Chromium Single Cell Multiome kit. In order to add gene annotation to the ATAC data, I am trying to install and use the “EnsDb.Mmusculus.v79” and “BSgenome.Mmusculus.UCSC.mm10” packages with bioconductor. The same ERROR has come up repeatedly whenever…

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Dementia with Lewy bodies post-mortem brains reveal differentially methylated CpG sites with biomarker potential

Weisman, D. & McKeith, I. Dementia with Lewy Bodies. Semin. Neurol. 27, 042–047 (2007). Article  Google Scholar  Foguem, C. & Manckoundia, P. Lewy Body Disease: Clinical and Pathological “Overlap Syndrome” Between Synucleinopathies (Parkinson Disease) and Tauopathies (Alzheimer Disease). Curr. Neurol. Neurosci. Rep. 2018 18:5 18, 1–9 (2018). CAS  Google Scholar …

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Obtaining directionality of pathways

Obtaining directionality of pathways 0 I am attempting to use R to extract biological pathway information from several different online databases (specifically KEGG, Wikipathways and Reactome) and use that information in a larger project I am working on where I am attempting to gauge levels of pathway functionality. An important…

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Bioinformatics Scientist Job – Karkidi

Experience 2-4 year Salary $170,000-$180,000 Location San Francisco, CA, USA Job Function Bioinformatics Scientist Industry Information Technology Qualification Degree in Computer Science, PhD Degree, Degree in Bioinformatics, Degree in Computational Biology, Degree in Computational Science, Degree in Biomedical Engineering Key Skills Bioconductor, CRISPR technology, Data science techniques, Large data sets,…

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Bioconductor – RUVnormalize

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see RUVnormalize. RUV for normalization of expression array data Bioconductor version: 3.4 RUVnormalize is meant to remove unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean…

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Interpreting time-series analysis with DESeq2 output

Interpreting time-series analysis with DESeq2 output 1 Hello all, I read and followed time course experiment mentioned in DESeq2 vignette bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments Please see attached figure which was generated with this model: LRT p-value: ‘~ strain + minute + strain:minute’ vs ‘~ strain + minute’ I have also generated a similar…

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Bioconductor – RLHub (development version)

DOI: 10.18129/B9.bioc.RLHub     This is the development version of RLHub; for the stable release version, see RLHub. An ExperimentHub package for accessing processed RLSuite data sets Bioconductor version: Development (3.17) | RLHub provides a convenient interface to the processed data provided within RLSuite, a tool-chain for analyzing R-loop-mapping data…

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Quantifying Peak Height Difference in ATAC-seq

Quantifying Peak Height Difference in ATAC-seq 1 Hi, everyone. How would I go about quantifying the peak height difference of a particular gene between two a wild type and a mutant in ATAC-seq? A colleague mentioned possibly calculating a moving average of read depths for smoothing and then comparing the…

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Nociceptor neurons affect cancer immunosurveillance

Secondary use of biopsies as research specimens The ten melanoma samples used in this study were collected by Sanford Health and classified by a board-certified pathologist. Their secondary use as research specimens (fully de-identified formalin-fixed, paraffin-embedded (FFPE) blocks) was approved under Sanford Health IRB protocol 640 (titled ‘Understanding and improving…

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Bioconductor – RTCA

Open-source toolkit to analyse data from xCELLigence System (RTCA) by Roche Bioconductor version: 2.5 Import, analyze and visualize data harvested from Roche(R) Xcelligence RTCA systems. The package imports the rich information in real-time cell electrical impedance data into computational and statistical environment R/Bioconductor. As an alternative to commercial software provided…

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Shared mechanisms and crosstalk of COVID-19 and osteoporosis via vitamin D

Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579(7798), 270–273. doi.org/10.1038/s41586-020-2012-7 (2020). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Lipsitch, M., Swerdlow, D. L. & Finelli, L. Defining the epidemiology of Covid-19—Studies needed. N. Engl. J. Med. 382(13), 1194–1196. doi.org/10.1056/NEJMp2002125…

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r – monocle3 installation issues

I have R 4.2.1 and the latest R studio build 554 on a macOS Monterey. I am trying to install monocle3 using the following : BiocManager::install(‘monocle3’) I get a really long error message BiocManager::install(“monocle3”) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.15…

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DESeq2 design formula considerations

nhaus – This question has been asked many times both here as well as on other fora, for instance the bioconductor forum. Mike Love (the author of the DESeq2 software) has probably answered this question 50-60 times, if I had to guess, so you can find a lot on this…

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r – Cannot install bioconductor DESeq2 package on M1 mac … any advice?

This is where the installation failed. I tried installing DESeq2 on “R Studio Cloud” and it worked. I am assuming this is a mac issue. If anyone knows what to do I would very much appreciate it! Very new to R so anything will help. make: /opt/R/arm64/bin/gfortran: No such file…

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Insights on the bacterial composition of Parmigiano Reggiano Pure Whey Starter by a culture-dependent and 16S rRNA metabarcoding portrait

Smid, E. J. et al. Practical implications of the microbial group construction of undefined mesophilic starter cultures. Microb. Cell Factories 13, S2. doi.org/10.1186/1475-2859-13-S1-S2 (2014). Article  Google Scholar  Stadhouders, J. & Leenders, G. J. M. Spontaneously developed mixed-strain cheese starters. Their behaviour in direction of phages and their use within the…

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Bioconductor – clusterExperiment

DOI: 10.18129/B9.bioc.clusterExperiment     Compare Clusterings for Single-Cell Sequencing Bioconductor version: Release (3.5) Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets. Author: Elizabeth Purdom [aut, cre, cph], Davide Risso [aut], Marla Johnson [ctb] Maintainer: Elizabeth Purdom <epurdom at…

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Bioconductor – MafH5.gnomAD.v3.1.1.GRCh38 (development version)

DOI: 10.18129/B9.bioc.MafH5.gnomAD.v3.1.1.GRCh38     This is the development version of MafH5.gnomAD.v3.1.1.GRCh38; for the stable release version, see MafH5.gnomAD.v3.1.1.GRCh38. Minor allele frequency data from gnomAD version 3.1.1 for GRCh38 Bioconductor version: Development (3.16) Store minor allele frequency data from the Genome Aggregation Database (gnomAD version 3.1.1) for the human genome version…

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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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