Tag: cran

I want to develop a private local package on a RStudio server but it seems configured in a way that makes that impossible. I know that as a simple user I cannot install a package from the outside (eg. CRAN or git). But I have been thinking that I can…

UK date and time: 07-June-2023 17:48 &nbsp Applicant Options New Search Login Job Details Help Terms of Use & Privacy Policy &nbsp Job Details Postdoctoral Researcher in Bioinformatics Department of Oncology, Weatherall Institute of Molecular Medicine, Headington, Oxford, OX3 9DS About the role Applications are invited from enthusiastic, motivated individuals…

DOI: 10.18129/B9.bioc.lpsymphony     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see lpsymphony. Symphony integer linear programming solver in R Bioconductor version: 3.13 This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming…

main content Veranstaltungsdaten 22. June 2023 09:00 – 22. June 2023 17:00 23. June 2023 09:00 – 23. June 2023 17:00 Philipps-Universität Marburg MARA F|05, Deutschhausstraße 11+13 Seminar room 01.0010 R is a widely used tool for data analyses. Part of its success is due to the active community and…

I am using Limma for downstream analysis of mass spectrometry proteomic data. I am comparing differential protein expression between healthy controls (n= 40) and two disease subtypes (disease_1 n= 59, disease_2 n= 41). I have an ‘intensities’ matrix with the log2 transformed LFQ expression for 1300 proteins in rows with…

*Install.packages(“tidyverse”) and install.packages(“ggplot2”) fails with non-zero exit status. I’ve tried using install.packages(“tidyverse”) and install.packages(“ggplot2”) but both ends in non-zero exit status. Part of the error reads Error i loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace ‘rlang’ 1.0.2 is being loaded, but >= 1.0.6 is required I’ve tried to remove.packages(“rLang”)…

Revsbech, N. P. et al. Determination of ultra-low oxygen concentrations in oxygen minimum zones by the STOX sensor. Limnol. Oceanogr.: Methods. 7, 371-381. (2009). Wright, J. J., Konwar, K. M. & Hallam, S. J. Microbial ecology of expanding oxygen minimum zones. Nat. Rev. Microbiol. 10, 381–394 (2012). Article  CAS  PubMed …

In this tutorial, I’ll try to provide a brief overview of the capabilities of our enrichment analysis R package pathfindR. The tool is in CRAN and its introductory vignette can be found here. We also have a detailed wiki. pathfindR is designed to improve enrichment analysis by firstly identifying active…

Is R the right tool for your data analysis needs? 1. A software for statistical computing and graphics R vs other statistical software such as SPSS, SAS, STATA, Mplus, HLM etc. : Pros Accessibility: R is free and open-source, while other statistical software like SPSS is proprietary software that requires…

Introduction Tropical rainforests in the Amazon basin harbor the highest tree diversity on earth (Ter Steege et al., 2020). Most of this diversity is concentrated in a relatively small number of plant families, including Chrysobalanaceae, Fabaceae, Lauraceae, Lecythidaceae, Malvaceae (sensu lato), Myrtaceae, Rubiaceae, and Sapotaceae, that can comprise > 60%…

R is a free and potent statistical software for analyzing and visualizing data. In this chapter, we provide a quick and straightforward introduction to R programming. What’is ROENTGEN and why learning RADIUS? Read show: What’is R and why teaching ROENTGEN? How R and RStudio Install R real RStudio on water…

Kiu, R. & Hall, L. J. An update on the human and animal enteric pathogen Clostridium perfringens. Emerg. Microbes Infect. 7, 141 (2018). Article  PubMed  PubMed Central  Google Scholar  Li, J., Paredes-Sabja, D., Sarker, M. R. & McClane, B. A. Clostridium perfringens sporulation and sporulation-associated toxin production. Microbiol. Spectr. doi.org/10.1128/microbiolspec.TBS-0022-2015…

We use Nexus as our internal repo. What configuration modifications do we need to make to route pip and cran calls inside JupyterHub to our internal Nexus repos. Hi. Do you mean you want to redirect calls made from a shell in a singleuser server such as JupyterLab to PyPI…

Keeping your software tools up-to-date is essential for a seamless and efficient workflow, and the R programming language is no exception. In this blog post, we will explore the importance of updating R, discuss the circumstances that may necessitate an update, address the possibility of updating R within RStudio, and…

Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, et al. Structure and function of the global topsoil microbiome. Nature. 2018;560:233–7. Article  CAS  PubMed  Google Scholar  Waldrop MP, Holloway JM, Smith DB, Goldhaber MB, Drenovsky RE, Scow KM, et al. The interacting roles of climate, soils, and…

Summary of genes and pathways in SMDB Using keywords (e.g., sulfur, sulfate) to retrieve 284,541 literature reports from 1976 to 2021 in Web of Science and then obtained records of sulfur genes through a web crawler with Python. After manual verification, 875 related literature reports (representative literature was recruited) and…

error which i recieve during dockerfile build is for R language 1: In install.packages(c(“tidyverse”), repos = “cran.rstudio.com/&#8221😉 : #8 7.643 installation of package ‘systemfonts’ had non-zero exit status #8 7.643 2: In install.packages(c(“tidyverse”), repos = “cran.rstudio.com/&#8221😉 : #8 7.643 installation of package ‘textshaping’ had non-zero exit status #8 7.643 3:…

I’m trying to use this code install.packages(“rgl”, repos = “http://cran.rstudio.com/”) install.packages(“ConsRank”, repos = “http://cran.rstudio.com/”) library(“ConsRank”) After installing some packages shows following error: NameError Traceback (most recent call last) <ipython-input-30-b36284337772> in <cell line: 1>() —-> 1 install.packages(“rgl”, repos = “http://cran.rstudio.com/”) 2 install.packages(“ConsRank”, repos = “http://cran.rstudio.com/”) 3 library(“ConsRank”) NameError: name ‘install’ is…

Abubucker, Sahar, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Mitreva, and Curtis Huttenhower. 2012. Metabolic reconstruction for metagenomic data and its application to the…

Chazot, N. et al. Priors and posteriors in Bayesian timing of divergence analyses: the age of butterflies revisited. Syst. Biol. 68, 797–813 (2019). Article  PubMed  PubMed Central  Google Scholar  Allio, R. et al. Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution. Syst. Biol. 69, 38–60…

Hi! I´m currently unable to install new packages in RStudio. I updated RStudio to the latest version and tried different CRAN repositories but still get the following error message: Error Information: Ausführung angehaltenERROR: lazy loading failed for package ‘bslib’ removing ‘C:/Users/anna-/Documents/R/win-library/3.6/bslib’Warning in install.packages :installation of package ‘bslib’ had non-zero exit…

At rstudio::conf(2022) our workshops featured hands-on exercises, discussions, and Q&A forums. This was an opportunity to meet, share, and collaborate with …In July, we wrapped up rstudio::conf(2022). Throughout the conference, we had an exciting array of workshops, an inspiring lineup of speakers, Birds of a …We are delighted to announce the rstudio::conf…

BioCann repository index warning on Apple Silicon (Bioc 3.17 / R 4.3) 0 @mjsteinbaugh Last seen 23 hours ago Cambridge, MA Hi Bioconductor team, I’m seeing a warning pop up during BiocManager::install calls on Apple Silicon related to the current BioCann repository index configuration. BiocManager::repositories() BioCsoft “https://bioconductor.org/packages/3.17/bioc” BioCann “https://bioconductor.org/packages/3.17/data/annotation” BioCexp…

Introduction Carbon nanotubes (CNTs) are nano-sized one-dimensional tubular structures rolled by single (single-walled CNTs, SWCNTs) or multiple layers (multi-walled CNTs, MWCNTs) of graphene with unique electrochemical, mechanical and thermal properties, which render them as attracted engineered nanomaterials for various commercial applications.1–4 An increase in the production and utilization of CNTs…

ggplot2.utils: Selected Utilities Extending ‘ggplot2’ Selected utilities, in particular ‘geoms’ and ‘stats’ functions, extending the ‘ggplot2’ package. Note that this package does not define the functions itself, but instead imports them from a collection of other packages and then exports them. These functions are tested as well to make sure…

install.packages(“ggplot2.utils”) 0.2.1 by Daniel Sabanés Bové, 8 hours ago insightsengineering.github.io/ggplot2.utils/ Report a bug at github.com/insightsengineering/ggplot2.utils/issues Browse source code at github.com/cran/ggplot2.utils Authors: Daniel Sabanés Bové [aut, cre] , F. Hoffmann-La Roche AG [cph, fnd] Documentation:   PDF Manual   Apache License 2.0 license Imports EnvStats, GGally, ggpp Depends on ggplot2 Suggests…

Hello, The installation of a Bioconductor package ShortRead in posit.cloud (free tier) fails due to apparent lack of permissions to write to /opt/R/4.3.0/lib/R/library/. I attach a screenshot of the error message (apologies for this, but I am solving someone else’s problem via screenshare). The project is posit.cloud/content/5941822 the command to…

In recent years, R has emerged as one of the most popular programming languages for data analysis and data science. Its popularity can be attributed to the increasing demand for data-driven insights and the need for more sophisticated statistical analysis tools.  Data analysis can be done using a variety of…

Cohen, J. M., Lajeunesse, M. J. & Rohr, J. R. A global synthesis of animal phenological responses to climate change. Nat. Clim. Chang. 8, 224–228 (2018). Park, D. S., Newman, E. A. & Breckheimer, I. K. Scale gaps in landscape phenology: challenges and opportunities. Trends Ecol. Evol. 36, 709–721 (2021)….

Global tuberculosis report 2020. (Geneva: World Health Organization; 2020. Licence: CC BY-NC-SA 3.0 IGO). Acuña-Villaorduna, C. et al. Intensity of exposure to pulmonary tuberculosis determines risk of tuberculosis infection and disease. Eur. Respir. J. 51, 1. doi.org/10.1183/13993003.01578-2017 (2018). Article  Google Scholar  Reichler, M. R. et al. Duration of exposure among…

Code in google colab: if (!require(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“TCGAbiolinks”) Error message: Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘help(“repositories”, package = “BiocManager”)’ for details. Replacement repositories: CRAN: cran.rstudio.com Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21) Installing package(s) ‘BiocVersion’, ‘TCGAbiolinks’ Warning…

Last updated on 2023-05-02 | Edit this page Expand All Solutions Questions How to find your way around RStudio? How to interact with R? How to manage your environment? How to install packages? Objectives Install latest version of R. Install latest version of RStudio. Navigate the RStudio GUI. Install additional…

After I installed on macOS, the new R version 4.3.0. I cannot update packages. RStudio shows me all my packages to update, but when I update them, they are installed in the (already installed) older version. A look into the index page Index of /bin/macosx/big-sur-x86_64 shows that the last update…

Code in google colab: if (!require(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“TCGAbiolinks”) Error message: Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘help(“repositories”, package = “BiocManager”)’ for details. Replacement repositories: CRAN: cran.rstudio.com Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21) Installing package(s) ‘BiocVersion’, ‘TCGAbiolinks’ Warning…

HI, I’m a total noob here so please go easy on me. My goal is to have JupyterHub/JupyterLab running on Docker inside an Azure Container Instance, and have a persistent Azure File Share mounted to the container instance. Some background. I’m using Docker Desktop (windows) to create the image. Then…

Song, S. J. et al. Preservation methods differ in fecal microbiome stability, affecting suitability for field studies. mSystems 1, e00021–16 (2016). Article  PubMed  PubMed Central  Google Scholar  Lauber, C. L., Zhou, N., Gordon, J. I., Knight, R. & Fierer, N. Effect of storage conditions on the assessment of bacterial community…

Introduction The metabolome is an incredibly diverse collection of small molecules (<1,500 Da) in biological systems involved in virtually every cellular process, including cellular energy production, macromolecule synthesis, epigenetic modifications, cell signalling and more (for recent reviews see [Citation1–6]). It responds rapidly (in seconds) to both internal (signalling, allostery) and external…

Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998). Article  CAS  PubMed  PubMed Central  Google Scholar  Herndl, G. J. & Reinthaler, T. Microbial control of the dark end of the biological pump. Nat. Geosci. 6, 718–724 (2013)….

Please, I just updated my version R from 4.2.2 to 4.3.0, and also R Studio. Now, when I want to reinstall my packages, I get the error message below in my console: [1/33] Installing cli… Error: package ‘cli’ is not available In addition: Warning messages: 1: In value[[3L]](cond) : restarting…

Here are some steps you can try: Check with your IT department to see if there are any firewall rules that may be blocking access to CRAN or preventing downloads of packages. You may need to provide them with a list of the domains and ports that need to be…

If anyone is looking for an easy way to label facets for reports or publications, the egg (CRAN) package has pretty nifty tag_facet() & tag_facet_outside() functions. library(ggplot2) p <- ggplot(mtcars, aes(qsec, mpg)) + geom_point() + facet_grid(. ~ am) + theme_bw(base_size = 12) # install.packages(‘egg’, dependencies = TRUE) library(egg) Tag inside…

Hello everybody!I have to reinstall Ubuntu and also Rstudio.After that, I can’t install any packages, at all.Here are some details sessionInfo()R version 4.2.3 (2023-03-15)Platform: x86_64-pc-linux-gnu (64-bit)Running under: Ubuntu 20.04.6 LTS Matrix products: defaultBLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 locale:[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=ru_RU.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=ru_RU.UTF-8[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=ru_RU.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C[11] LC_MEASUREMENT=ru_RU.UTF-8 LC_IDENTIFICATION=C attached base…

Baumgart, D. C. & Sandborn, W. J. Inflammatory bowel disease: Clinical aspects and established and evolving therapies. Lancet 369(9573), 1641–1657 (2007). Article  CAS  PubMed  Google Scholar  Baumgart, D. C. The diagnosis and treatment of Crohn’s disease and ulcerative colitis. Deutsches Aerzteblatt Online 106(8), 123–133 (2009). Google Scholar  Conrad, K., Roggenbuck,…

Last updated on 2023-04-18 | Edit this page Estimated time NA minutes Expand All Solutions Questions How do I install Bioconductor packages? How do I check if newer versions of my installed packages are available? How do I update Bioconductor packages? How do I find out the name of packages…

Error in getCdfInfo(object) : 1 @bca66a4b Last seen 1 hour ago Japan Hi I wanted to do a rma analysis for a affymetrix microarray data. but I got a problem. Code should be placed in three backticks as shown below setwd(“~/Downloads/GSE24184_RAW/”) library(affy) library(makecdfenv) data = ReadAffy() data and I got…

At rstudio::conf(2023) our workshops featured hands-on exercises, discussions, and Q&A forums. This was an opportunity to meet, share, and collaborate with …In July, we wrapped up rstudio::conf(2023). Throughout the conference, we had an exciting array of workshops, an inspiring lineup of speakers, Birds of a …We are delighted to announce the rstudio::conf…

Issue in installing any package in R 0 Hello everyone! I am facing a very weird issue. I am working on hpc where R is preinstalled. As I am trying to install any package, I am getting this error: **Warning message: package ‘BiocManager’ is not available for this version of…

 Sure, I’d be happy to help you download R and install RStudio on your Macbook with the M1 chip running Big Sur. Here are the step-by-step instructions: Image Credit: Google Step 1: Download R Go to the R Project website (www.r-project.org/) and click on the “Download R” link on the…

I originally want to use R-Swat for work and I followed the instruction to install R-Swat. It asked me to add install package “numbers” *> runGitHub(“R-SWAT”,”tamnva”) Downloading github.com/tamnva/R-SWAT/archive/HEAD.tar.gz Error: package or namespace load failed for ‘sensitivity’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘numbers’ type…

RStudio has emerged as a powerful integrated development environment (IDE) tailored for data science and statistical computing. With its user-friendly interface and extensive functionality, RStudio has become a popular choice for professionals and enthusiasts alike. In this article, we will explore how to download and install RStudio on Mac. Moreover,…

RStudio has evolved into a powerful integrated development environment (IDE) designed for data science and statistical computing. With its user-friendly interface and extensive functionality, RStudio has become a popular choice for professionals and enthusiasts. In this article, we will explore how to download and install RStudio on Mac. Additionally, we’ll…

RStudio has evolved into a powerful integrated development environment (IDE) tailored for data science and statistical computing. With its user-friendly interface and extensive functionality, RStudio has become a popular choice for professionals and enthusiasts alike. This article will show you how to download and install RStudio on Mac. In addition,…

Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380–382 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Milani, C. et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol. Mol. Biol. Rev. 81, e00036-17…

Hi , I have been running SKAT test to get gene-level-based pvalues of a dichotomous phenotype. I used this documentation : rdrr.io/cran/SKAT/man/SKAT.html this is my code : for (gene in genes) { # skip genes with only one SNP #if (num_snps == 1) { # next #} print(gene) # extract…

Hi , im trying to preorm SKAT test (rdrr.io/cran/SKAT/man/SKAT.html) for every gene in my data . in order to do that for every gene i created the genetype matrix which has 21 rows ( as number of patients) and columns as number of SNPs for every gene . this is…

This isn’t an answer in the sense that this will help you further your goal, but perhaps it might help you scope out a different goal. The reason that waldo is reporting differences between these plots, is because upon addition of every layer, the scales are cloned: the new scales…

I have seen this issue being recurrent and tried many options for the last two days but non yielded to correct installation of any of these packages. I used BiocManager as suggested in other issues, also tried to install from local source, nothing seems to be working. This issue started…

## — The problem: — I’m trying to run Rstudio, but whenever I start up I see these messages: During startup – Warning messages: 1: Setting LC_CTYPE failed, using “C” 2: Setting LC_COLLATE failed, using “C” 3: Setting LC_TIME failed, using “C” 4: Setting LC_MONETARY failed, using “C” Which I…

Bioinformatics is a rapidly growing field that integrates biological science and computer science for the development and application of computational tools in order to analyze and interpret biological data. Programming languages are the most fundamental and versatile tool that has become essential in bioinformatics. There are various languages that are…

I’m trying to install the package ggplot2 on R but it gives me a warning saying that I have to install Rtools. I did it, but it still gives me the same warnings saying that I have to install Rtools. What do I have to do after installing Rtools? And…

To update R using RStudio, you can follow these steps: Install the installr package (Windows only) or use the updateR() function from the rstudioapi package (macOS and Linux). Run the appropriate function to update R. Restart RStudio. Please note that the installr package is available only for Windows. If you’re…

My original problem is my attempt to load the ggplot2 package, which failed because my rlang package is too old and is using the binary version instead of the source version. When I attempt to update rlang (or most packages, really,) I usually receive the following message: WARNING: Rtools is…

O’Neill J. The Review on Antimicrobial Resistance—tackling drug-resistant infections globally: final report and recommendations. 2016. Murray CJ, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet. 2022;399:629–55. Article  CAS  Google Scholar  Laxminarayan R….

Kirchberger PC, Schmidt ML, Ochman H. The ingenuity of bacterial genomes. Annu Rev Microbiol. 2020;74:815–34. Article  CAS  PubMed  Google Scholar  Rodríguez-Gijón A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, et al. A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked…

I was trying to install ExomeDepth pacakge, after that one of its command from its document getBamCounts gives following error. Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace ‘rlang’ 1.0.5 is already loaded, but >= 1.1.0 is required Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): namespace ‘rlang’…

Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3:754–66. Article  CAS  PubMed  Google Scholar  Suttle CA. Marine viruses—major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–12. Article  CAS  PubMed  Google Scholar  Breitbart M. Marine viruses: truth or dare. Ann…

R: Open R Script, R Markdown script, or SQL Script in RStudio script.open {misty} R Documentation Open R Script, R Markdown script, or SQL Script in RStudio Description This function is used to open an R script, R markdown script, or SQL script in RStudio. Usage script.open(path, line = 1,…

hi, I have data that looks like this: 3-column SNPs their gene based on Annovar and a p-value for every SNP. What I would like is to aggregate the p values for every gene. snps <- data.frame( snp_id = c(“rs1”, “rs2”, “rs3”, “rs4”, “rs5”, “rs6”, “rs7”, “rs8”), Gene.refGene_ANNOVAR = c(“gene1”,…

At rstudio::conf(2023) our workshops featured hands-on exercises, discussions, and Q&A forums. This was an opportunity to meet, share, and collaborate with …In July, we wrapped up rstudio::conf(2023). Throughout the conference, we had an exciting array of workshops, an inspiring lineup of speakers, Birds of a …We are delighted to announce the rstudio::conf…

Hello, am following this page to make multiple R installation available. $ rstudio-server version 2021.09.0+351 (Ghost Orchid) for CentOS 8 Steps I’ve done rstudio-server stop cd /etc/rstudio touch r-versions chmod g+rwx,o+rwx /etc/rstudio/r-versions chmod -t /etc/rstudio/r-versions Modify r-versions with the following lines Path: /opt/R/4.2.2 Label: CRAN R422 Path: /opt/microsoft/ropen/4.0.2/lib64/R Label: MRAN…

Easy web publishing from R. Write R Markdown documents in RStudio. Share them here on RPubs. (It’s free, and couldn’t be simpler!)RStudio lets you harness the power of R Markdown to create documents that weave together your writing and the output of your R code. And now, with RPubs, you …RPubs…

Simes method 0 Hi Hi , I have data that has 3 column SNPs their gene based on Annovar and a pvalue for every SNP . What I would like is to aggregate the p values for every gene. I used simes method in R : rdrr.io/cran/mppa/man/simes.test.html: and this is…

Haley Jeppson (Department of Statistics) , Heike Hofmann (Department of Statistics) 2023-03-09 Graphical methods for categorical variables are not as thoroughly developed when compared with what is available for numeric variables. Categorical variables in scientific publications often appear in the form of bar charts (first published in the Commercial and…

No BSgenome for Human HG19 or HG38 with R version 4.2.2 and Bioconductor 3.16 1 @aac4f0b4 Last seen 17 hours ago France Hello, I’m currently trying to install BSgenome.Hsapiens.UCSC.hg19 and BSgenome.Hsapiens.UCSC.hg38 through bioconductor on my desktop (Windows) My current R version is 4.2.2.and bioconductor is 3.16 My command is this…

Transcribed image text: Question 1. Consider the Boston dataset from the textbook “An Introduction to Statistical Learning’ containing housing values in 506 suburbs of Boston; see https: //cran.rstudio.com/web/packages/ISLR2/ISLR2.pdf. The aim is to predict the housing values (response variable: medv) using the remaining variables as covariates. [total: 25 marks] (a) Randomly…

You must have .R or RStudio to do these problems. (I made a link to the .R files for each question)   the link for .R’s website is here:cran.r-project.org/bin/windows/base/   Maybe you have them already, I tried to convert them into .csv files (for Excel or Minitab which I prefer)…

I am currently building a package which uses the “limma”-package as a dependency. I want to submit my package to CRAN. Do I need to declare Bioconductor-dependencies such as Limma differently in the Description-File of my Package? The Check-Function in R shows no Notes, Warnings or Errors, but I am…

Hi, I am on bullseye and am trying to install the package r-cran-ggplot2. This fails with E: Failed to fetch deb.debian.org/debian/pool/main/p/postgresql-13/libpq5_13.8-0%2bdeb11u1_amd64.deb 404 Not Found [IP: 146.75.122.132 80] (full output below). There seems to be a dependency on libpq5 version 13.8 whereas the version available for bullseye is 13.9. Any ideas how to…

ClimInd package computes climate indices. Even though package functions are simple, I receive errors when I use with dataframe data. Package page (in Cran), doesn’t provide any info on what data we are suppose to use in order to get an output. More specifically, function sdii() has the following form:…

Inagaki, F., Takai, K., Kobayashi, H., Nealson, K. H. & Horikoshi, K. Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing e-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 53, 1801–1805 (2003). Article  CAS  PubMed  Google Scholar  Timmer-Ten Hoor, A. A new type of…

Hi All,I’m having difficulty configuring proxy that will allow me to download packages from CRAN. I’ve reviewed the help files, but can’t get it to work. I’m probably doing it wrong because I dont know how to get to or modify this /etc/rstudio-connect/rstudio-Can someone walk me through how to configure…

I’m trying to use an RStudio Docker image to install an R package, but I receive this error message: install.packages(‘tidyverse’) Warning in install.packages : unable to access index for repository packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib: cannot open URL ‘https://packagemanager.posit.co/cran/__linux__/jammy/latest/src/contrib/PACKAGES’ Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) Warning in install.packages : unable to access…

This workshop is part of UNM’s Research Data Services Coffee & Code workshop series that focus on tools and strategies that make data management, analysis, visualization, communication, and sharing more efficient and more fun. This workshop will will provide a hands-on introduction to the R analytic programming language and the RStudio Integrated Development Environment…

excluded in the analysis. Solve optimization problems using an R interface to NLopt. The overall false discovery rate is controlled by the mdFDR methodology we In this formula, other covariates could potentially be included to adjust for confounding. depends on our research goals. W, a data.frame of test statistics. enter…

Cant install packages > install.packages(“tidyverse”) Warning in install.packages : unable to access index for repository cran.rstudio.com/src/contrib: cannot open URL ‘http://cran.rstudio.com/src/contrib/PACKAGES’ this is what i have tried so far i have tried using a CRAN repository closer to me (im in sydney australia) – this didnt help i have tried downloading…

Overview The BiocManager package, as the modern successor package to BiocInstaller, allows users to install and manage packages from the Bioconductor project. Bioconductor focuses on the statistical analysis and comprehension of high-throughput genomic data. Current Bioconductor packages are available on a ‘release’ version intended for every-day use, and a ‘devel’…

I have a nextflow workflow for which I am running with sge + apptainer profile using the command nextflow run main.nf -profile sge,apptainer but I am receiving the error line #: bwa: command not found I have tried running apptainer run workflow.sif to check, and bwa as well as other…

At rstudio::conf(2022) our workshops featured hands-on exercises, discussions, and Q&A forums. This was an opportunity to meet, share, and collaborate with …In July, we wrapped up rstudio::conf(2022). Throughout the conference, we had an exciting array of workshops, an inspiring lineup of speakers, Birds of a …We are delighted to announce the rstudio::conf…

Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193–199 (2009). Article  CAS  PubMed  Google Scholar  Graham, E. B. et al. Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Front. Microbiol. 7, 214 (2016). Article  PubMed  PubMed Central  Google Scholar …

Automated unit testing of Shiny applications through a headless ‘Chromium’ browser. Version: 0.2.1 Depends: testthat (≥ 3.1.2) Imports: R6 (≥ 2.4.0), callr, checkmate (≥ 2.0.0), chromote (≥ 0.1.0), crayon, ellipsis, fs, globals (≥ 0.14.0), httr, jsonlite, pingr, rlang (≥ 0.3.0), rmarkdown, shiny, withr LinkingTo: cpp11 Suggests: deSolve, diffobj, ggplot2, knitr,…

Embeds the SQLite database engine in R, providing a DBI-compliant interface. SQLite is a public-domain, single-user, very light-weight database engine that implements a decent subset of the SQL 92 standard, including the core table creation, updating, insertion, and selection operations, plus transaction management. You can install the latest released version…

Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 71, 209–249 (2021). Article  PubMed  Google Scholar  Sanli, O. et al. Bladder cancer. Nat. Rev. Dis. Prim. 3, 17022 (2017). Article  PubMed  Google Scholar  International…

Hi, I’m hoping to get a package ready for the 3.17 Bioconductor release but I am unable to get a functional GO.db package for the devel version > BiocManager::install(version=’devel’) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.17 (BiocManager 1.30.19), R Under development…

Hunter, D. J. & Bierma-Zeinstra, S. Osteoarthritis. Lancet 393, 1745–1759 (2019). Article  CAS  Google Scholar  Hunter, D. J., March, L. & Chew, M. Osteoarthritis in 2020 and beyond: A Lancet Commission. Lancet 396, 1711–1712 (2020). Article  Google Scholar  Puig-Junoy, J. & RuizZamora, A. Socio-economic costs of osteoarthritis: A systematic review…

I need to install Devtools so i can donwload the 0.5.4 htmltools package from github, almost every package i try to install gives an error stating that the htmltools version i have is 0.5.2 but the package requires the 0.5.4 version, which i think is the github developers version, but…

installation of bioclite gives an error 1 Hello everyone, I am trying to install biocLite using BiocManager::install function in rstudio but its giving me an error. BiocManager::install(“biocLite”) Warning message: package ‘biocLite’ is not available for Bioconductor version ‘3.16’ A version of this package for your version of R might be…

CRAN Package Check Results for Package onetime CRAN Package Check Results for Package onetime Last updated on 2023-02-07 21:54:24 CET. Check Details Version: 0.1.0 Check: Rd cross-references Result: NOTE     Undeclared package ‘lubridate’ in Rd xrefs Flavor: r-devel-linux-x86_64-fedora-clang Version: 0.1.0 Check: for unstated dependencies in ‘tests’ Result: WARN     Warning: unable to…

It has been reported that genes are not independent of each other, co-expressed genes may have similar biological functions, and the effect of grouping genes is relatively strong17. WGCNA algorithm, which has been widely used for studying network changes, can be used to identify network topologies and sub-networks (called modules),…

phylogeny 2 Dear all， I am a student in the field of phylogeny.I calculated the phylogenetic diversity with R Language.I I encountered the above problem.Maybe there’s something wrong with my phylogenetic tree.I wish to ask teachers to help me solve this problem. Thanks a lot！！！ Error in node.age(sub.tree) : function…

1 Introduction Cervical cancer (CC) remains the fourth most common cancer in women worldwide, with 604,127 new cases in 2020 and more than 341,831 deaths, accounting for nearly 8% of all female cancer-related deaths annually (Sung et al., 2021). This common infection-related neoplasm and its premalignant precursor are caused by high-risk…