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Tag: cran
Deseq2 output and robust PCA (PcaGrid and PcaHubert)
Deseq2 output and robust PCA (PcaGrid and PcaHubert) 0 Hello there, I followed the deseq2 file to get the list of differentially expressed genes of a dataset I am working on. The Pca graph I got was not enough to show which one of the replicate is an outlier. A…
Detection of DNA methylation signatures through the lens of genomic imprinting
Animals and samples The study included 10 pigs, 8 pigs were bred at the INRAE experimental farm (doi.org/doi.org/10.15454/1.5572415481185847E12) and 2 pigs come from breeding organizations in accordance with the French and European legislation on animal welfare. The animals belong to the same family, except for one LW animal. Animals were…
Having Trouble Loading Required Packages : Lazy-Load database is corrupt – General
Hi, I am very new to R-Studio but a few months I had taken an 8-week course in which I was taught to use R-Studio for academic purposes. I recently decided to review some of the exercises we were provided with. However, I have now started to have trouble loading…
Installing R and Setting Up RStudio
Here, we will discuss how to install R and set up RStudio. R is an open-source and free to use application primarily used for computing, data analysis, data visualization and statistical analysis. R offers variety of functionalities that includes but not limited to: You can install R at www.r-project.org. Click…
Topic Modeling using R-Studio
1. Importing text 2. Cleaning the text 3. Counting the words and Visualization (Wordcloud, Wordcloud2, Comparison Cloud) 4. Sentiment Analysis 5. Topic Modeling 6. Predictive Analysis In the first playlist, I’ve explained the nuances of a R-package QUANTEDA which is a comprehensive package and contains almost all capabilities of other packages. There…
rstudio – Cannot deploy R-shiny app due to “fribidi was not found”
Local app runs fine, but I keep encountering this error when attempting to publish it. I have already installed fribidi & harfbuzz using brew install fribidi & brew install harfbuzz on my Mac, but I am still encountering the error. I am using: Installing urltools (1.7.3) … Using cached urltools….
Error In Library(Shiny) ‘Shiny’ Is Not A Valid Installed Package at David Lord blog
Error In Library(Shiny) ‘Shiny’ Is Not A Valid Installed Package. However, not sure i get this message. Package or namespace load failed for shiny : shiny upload file example “Error an error had occured. Check your – image credit : community.rstudio.com It means that…
Video Tutorials for An R Companion to Political Analysis, 3rd Edition
Additional Resources Quantitative Research Methods for Political Science, Public Policy and Public Administration Web site for book, based on R, by Jenkins-Smith et al. Swirl Stats Teaches you R programming and data science interactively, at your own pace, and right in the R console Dartistics: Digital Analytics with R and…
A super-pangenome of the North American wild grape species | Genome Biology
Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…
Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout
FAO. The State of World Fisheries and Aquaculture 2022: Towards Blue Transformation (FAO, 2022). Google Scholar Hua, K. et al. The future of aquatic protein: Implications for protein sources in aquaculture diets. One Earth 3, 316–329 (2019). Article Google Scholar Hardy, R. W. Utilization of plant proteins in fish diets:…
Accessing Snowflake with R Studio via ODBC on SPCS | by Gabriel Mullen | Snowflake | Dec, 2023
In a previous post, I was able to deploy a R Studio container into Snowpark Container Service. This allows me to run R code directly in Snowflake, but I still need to connect to Snowflake to grab data. So when I attempted to use the dbConnect syntax from the original…
Building an Advanced Web Scraper for Kaggle Leaderboards Using RSelenium
Machine learning is only possible when there’s enough of data available. Data collection is one of the most vital components of the machine learning lifecycle, but it’s also the one that’s often overlooked. Web scraping—programmatically collecting data from web pages—is often the primary technique used to collect information from the…
Importing Data In RStudio: A Step-By-Step Approach
Article Summary Box Recognizing various data types like numeric, integer, and logical in RStudio is essential for accurate data manipulation and import. Effective environment setup, including package installation and global option configuration, is pivotal for streamlined data import processes. Utilizing data.table’s fread function for handling large datasets enhances import efficiency,…
Tax4Fun2 package are not found and github repository is not maintained anymore
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore 5 Hi everyone! I have tried to find the R package Tax4Fun2 from the paper (pubmed.ncbi.nlm.nih.gov/33902725/) . This R package lets analizes the microbiome in an easy way to predict functional profiles from metagenomic 16S rRNA data….
Efficient Ways To Get Help On An R Package In RStudio
Article Summary Box Familiarize yourself with RStudio’s help system, which is essential for efficient programming. Strategies for accessing detailed documentation for specific R packages directly within RStudio. Leverage RStudio’s advanced search features for streamlining the process of finding relevant help information. Interpreting and utilizing package vignettes and manuals, an often-overlooked…
Loading R Packages In RStudio: A Step-By-Step Approach
Article Summary Box Preparing RStudio for package management is pivotal, involving setting up workspace directories and ensuring R version compatibility for optimal package functionality. In Understanding Package Libraries, the intricacies of library paths and package storage locations reveal strategies for streamlined package accessibility and organization. Advanced Techniques for Package Loading…
Installing R Packages In RStudio: A Step-By-Step Approach
Article Summary Box RStudio’s Package Manager significantly simplifies the process of installing and managing R packages, enhancing user efficiency. CRAN’s vast repository offers a wide range of R packages, but understanding the nuances of package versions and dependencies is crucial for optimal utilization. Utilizing GitHub for R package installations opens…
RMC lab file R Studio.docx – INTRODUCTION TO R Studio Q1. How to Install R Studio? What is the latest version of R. Give details? Q2. RStudio Layout
INTRODUCTION TO R Studio Q1.How to Install R Studio? What is the latest version of R. Give details? Q2.RStudio Layout with snapshot. Explain the purpose of all panes Q3.Who designed and developed the R language? Q4.Are variables ‘H’ and ‘h’ same in R language? Q5.What is a package? What are…
Navigating TensorFlow Configuration in RStudio: A Guide for Diverse Environments | by Kamrul | Dec, 2023
1. Installing the Right Python Version Recommended Version: Python 3.10.x Optimal balance between new features and stability. Compatible with TensorFlow and avoids many common issues. Installation: Visit the Python website and select a 3.10.x version. Verification: python –version Troubleshooting: Ensure Python is correctly added to your system PATH. 2. Installing…
sparklyr – Databricks Connect v2
Last updated: Thu Dec 7 16:28:19 2023 Intro Databricks Connect enables the interaction with Spark clusters remotely. It is based on Spark Connect, which enables remote connectivity thanks to its new decoupled client-server architecture. This allows users to interact with the Spark cluster without having to run the jobs from…
Rstudio cloud
Rstudio cloud 1 Dear fellows, a bit off topic today. I am just starting to use R studio cloud from a supercomputer to analyze my single cell and have recently experienced issue with installing packages. Not sure whether anyone have any experience installing packages in R studio cloud and could…
Bioconductor Code: CelliD
# CelliD v0.99 R package for gene signature extraction and cell identity recognition at individual cell level from single-cell RNA-seq. ![logo](https://github.com/RausellLab/CelliD/blob/gh-pages/tools/sticker.png?raw=true) —————————————- Welcome to the official Github repository of the **CelliD** software presented in the Article [Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID, Nature…
ios – How to install package “marked” on RStudio?
I’ve tried installing packages specific to my studies ( BayesFactor and marked ) but each time it ask fro a “sub”package ( Matrix and lme4 ) and it always give me a code line where I can seems to use the sub package. the end line is always : ‘/private/var/folders/6n/5bhjfv893xggr98bhctym2sr0000gn/T/Rtmp7wjqtG/downloaded_packages’…
Zea mays genotype influences microbial and viral rhizobiome community structure
Oburger E, Schmidt H. New methods to unravel rhizosphere processes. Trends Plant Sci. 2016;21:243–55. Article CAS PubMed Google Scholar Rout ME, Southworth D. The root microbiome influences scales from molecules to ecosystems: the unseen majority. Am J Bot. 2013;100:1689–91. Article PubMed Google Scholar Pratama AA, Terpstra J, de Oliveria ALM,…
vcftools’ –weir-fst-pop and R hierfstats package’s varcomp.glob()
Differing output: vcftools’ –weir-fst-pop and R hierfstats package’s varcomp.glob() 0 I’m getting different Fst values when I use vcftools –weir-fst-pop vs. the varcomp.glob() function from the R hierfstats package. I’m not sure why because they both calculate Fst based on Weir & Cockerham’s 1984 paper. Can someone please explain why?…
Package Prefix double-colon notation in user-created package – Package development
Our team created a user-defined R package for a project. When we created this package, we did so on a Windows OS and included the name of the package we built as a prefix whenever we call one of its R functions (e.g., dplyr::filter()). However, now that our RStudio server…
How to Install R and RStudio – Dr Isabella Gollini How to Install R and RStudio 1 Install R In order
Dr Isabella Gollini How to Install R and RStudio 1 Install R In order to install R follow the following commands: go to cran.rstudio/ depending of your operating system click on: click Download R for Linux choose you Linux distribution and follow the instructions given on the website click Download…
Is R better than Python?
Title: Exploring the Distinct Strengths of R and Python: A Comparative Analysis Introduction:In the world of data science and statistical analysis, two programming languages have emerged as frontrunners: R and Python. Both languages offer unique features and capabilities that cater to different needs and preferences. While some argue that R…
Why is DMRcate not available for Bioconductor version 3.18?
Why is DMRcate not available for Bioconductor version 3.18? 0 @daniel-e-weeks-10677 Last seen 22 hours ago Pittsburgh, Pennsylvania, United States… According to the Bioconductor web page for DMRcate, it looks like it is available for Bioconductor version 3.18 but this installation fails: > BiocManager::install(“DMRcate”) Bioconductor version 3.18 (BiocManager 1.30.22), R…
RStudio For Quantitative Finance
Introduction to RStudio R is widely used in quantitative finance due to its extensive statistical capabilities, data manipulation tools, and its active community that develops and maintains specialized packages for finance. It offers a wide range of functionalities that enable professionals in the finance industry to analyze data, build models,…
Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability
Szekanecz, Z. et al. Autoinflammation and autoimmunity across rheumatic and musculoskeletal diseases. Nat. Rev. Rheumatol. 17, 585–595 (2021). Article CAS PubMed Google Scholar Rosenblum, M. D., Remedios, K. A. & Abbas, A. K. Mechanisms of human autoimmunity. J. Clin. Invest. 125, 2228–2233 (2015). Article PubMed PubMed Central Google Scholar Wang,…
MSL2 ensures biallelic gene expression in mammals
Materials Animals All of the mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics. The mice were maintained under specific-pathogen-free conditions, with 2 to 5 mice housed in individually ventilated cages (Techniplast). The cages were equipped with bedding material, nesting material, a paper…
FVA on Sybil
FVA on Sybil 1 Does anyone know how to access the numeric results after using fluxVar() in Sybil ? I’m hopping for something similar to what you get with Cobratoolbox and fluxVariability() Im using the ec_core SBML for the example So far I have: Fluxv<-fluxVar(ec_core) values<-round(lp_obj(Fluxv),4) This results in a…
Rstudio cant install packages – General
Hi together i am currently doing an introductory course in R but having trouble with Rstudio.i want to install a package but just get a really, really long error.Below is what i get in return but i’m already struggling to understand the first bit because i have got rtools installed…
linux – cannot install R package in Rstudio cloud
I am just starting using Rstudio Cloud in Linux and encountered issue installing the package. I just started with tidyverse #install tidyverse packages options(repos = c(CRAN = “https://cloud.r-project.org”)) options(download.file.method = “libcurl”) install.packages(“tidyverse”) #Error I got > install.packages(“tidyverse”) Warning in install.packages : unable to access index for repository cloud.r-project.org/src/contrib: cannot open…
Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach
Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol. 2020;70:5607–12. Article PubMed PubMed Central Google Scholar Saxena AK, Kumar M, Chakdar H, Anuroopa N, Bagyaraj DJ. Bacillus species in soil…
Raising money to package RStudio for the Nix package manager for macOS platforms – RStudio IDE
Dear community I am doing a Gofundme to raise the money required to package Rstudio for macOS platforms for the Nix package manager. Nix is a package manager that can be installed on Windows (through WSL2), Linux and macOS. If you’ve been using package managers on macOS, you might be…
How To Read Data In R
Source: Ytimg.com Are you interested in analyzing and extracting insights from data using R? If so, learning how to read data in R is a fundamental skill that will empower you to explore and manipulate datasets effectively. R, a powerful programming language and software environment for statistical computing, provides various…
Bioconductor Code: SNPRelate
SNPRelate: Parallel computing toolset for relatedness and principal component analysis of SNP data ==== ![GPLv3](http://www.gnu.org/graphics/gplv3-88×31.png) [GNU General Public License, GPLv3](http://www.gnu.org/copyleft/gpl.html) [![Availability](http://www.bioconductor.org/shields/availability/release/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![Years-in-BioC](http://www.bioconductor.org/shields/years-in-bioc/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![R](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml/badge.svg)](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml) ## Features Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed SNPRelate (R…
Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced
Vicia sepium L. (bush vetch, Fabaceae) is a small perennial herb that is widely distributed on the Eurasian continent in the temperate Euro-Siberian broad-leaved forest region1. It has a wide distribution, both horizontally and vertically; for example, in the Swiss Alps, it grows from the lowlands to the sub alpine…
How To Create Dashboards In R: A Step-By-Step Approach
Dashboards are essential tools for visualizing data effectively, and R offers robust capabilities to build them. This guide provides a step-by-step approach to creating interactive, user-friendly dashboards in R, tailored to meet the specific needs of developers and programmers. Setting Up The Environment Designing The Dashboard Layout Adding Interactive Elements…
#1056648 – ITP: r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats
#1056648 – ITP: r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats – Debian Bug report logs Reply or subscribe to this bug. Toggle useless messages Report forwarded to debian-bugs-dist@lists.debian.org, r-pkg-team@alioth-lists.debian.net, wnpp@debian.org:Bug#1056648; Package wnpp. (Fri, 24 Nov 2023 11:00:03 GMT) (full text, mbox, link). Acknowledgement sent to Andreas Tille…
r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats
Package: wnpp Severity: wishlist Subject: ITP: r-cran-ggstats — GNU R extension to ‘ggplot2’ for plotting stats Package: wnpp Owner: Andreas Tille <ti…@debian.org> Severity: wishlist * Package name : r-cran-ggstats Version : 0.5.1 Upstream Author : Joseph Larmarange * URL : cran.r-project.org/package=ggstats * License : GPL-3+ Programming Lang: GNU R Description…
r-studio: “warning in install.packages: installation of package “spant” had non-zero exit status” problem
running R (version 4.2.2) and R Studio (version 1.4.1717), with 10GB of memory. trying to install the toolbox “spant” on HPC (high performance computer) cluster, and i get this error > Warning in install.packages: installation of package “spant” had non-zero exit status what am i missing to fix this? i…
Analyzing somatic mutations by single-cell whole-genome sequencing
Failla, G. The aging process and cancerogenesis. Ann. N. Y. Acad. Sci. 71, 1124–1140 (1958). Article CAS PubMed Google Scholar Szilard, L. On the nature of the aging process. Proc. Natl Acad. Sci. USA 45, 30–45 (1959). Article CAS PubMed PubMed Central Google Scholar Vijg, J. & Dong, X. Pathogenic…
R ggplot2::layer — EndMemo
R layer — ggplot2 A layer is a combination of data, stat and geom with a potential position adjustment. Usually layers are created using geom_* or stat_* calls but it can also be created directly using this function. ggplot2::layer is located in package ggplot2. Please install and load package ggplot2…
Accepted r-cran-rsqlite 2.3.3-1 (source) into unstable
—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Tue, 21 Nov 2023 21:04:55 +0100 Source: r-cran-rsqlite Architecture: source Version: 2.3.3-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-cran-rsqlite (2.3.3-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: b8701a7d846703ed341b6d9f0da1772ede7b0025 2403 r-cran-rsqlite_2.3.3-1.dsc ce7d7f21085580a6ea1bd9790f621aecd23c170b…
Unraveling the mitochondrial phylogenetic landscape of Thailand reveals complex admixture and demographic dynamics
Higham, C. Early Mainland Southeast Asia (Antiquity (River Books Press Dist A C, 2014). Google Scholar O’Connell, J. F. et al. When did homo sapiens first reach Southeast Asia and Sahul?. Proc. Natl. Acad. Sci. U. S. A. 115, 8482–8490 (2018). Article ADS PubMed PubMed Central Google Scholar Freidline, S….
Functional convergence of genomic and transcriptomic architecture underlies schooling behaviour in a live-bearing fish
Krause, J. & Ruxton, G. D. Living in Groups (Oxford Univ. Press, 2002). Réale, D., Reader, S. M., Sol, D., McDougall, P. T. & Dingemanse, N. J. Integrating animal temperament within ecology and evolution. Biol. Rev. 82, 291–318 (2007). Article PubMed Google Scholar Gartland, L. A., Firth, J. A., Laskowski,…
R sample.ped — EndMemo
R sample.ped Two pedigrees of different size for testing pedigree operations. sample.ped is located in package kinship2. Please install and load package kinship2 before use. data(sample.ped) install.packages(“kinship2″, repo=”http://cran.r-project.org”, dep=T) library(kinship2) data(sample.ped) Format: A data frame with 55 observations on the following 7 variables. ped pedigree id id subject id, unique…
R scale_type — EndMemo
R scale_type You will need to define a method for this method if you want to extend ggplot2 to handle new types of data. If you simply want to pass the vector through as an additional aesthetic, return “identity”. scale_type is located in package ggplot2. Please install and load package…
R register_theme_elements — EndMemo
R register_theme_elements The underlying structure of a ggplot2 theme is defined via the element tree, which specifies for each theme element what type it should have and whether it inherits from a parent element. In some use cases, it may be necessary to modify or extend this element tree and…
R summary.ggplot — EndMemo
R summary.ggplot Displays a useful description of a ggplot object. summary.ggplot is located in package ggplot2. Please install and load package ggplot2 before use. ## S3 method for class ‘ggplot’ summary(object, …) object ggplot2 object to summarise … other arguments ignored (for compatibility with generic) install.packages(“ggplot2″, repo=”http://cran.r-project.org”, dep=T) library(ggplot2) p…
R comp.score — EndMemo
R comp.score The function empirically estimate the variance of the score functions. The variance-covariance matrix consists of two parts: the additive part and the part for the individual-specific environmental effect. Other reasonable decompositions are possible. This program has the following improvement over “score.r”: 1. It works with selected nuclear families…
R launch_shinystan — EndMemo
R launch_shinystan Launch the ‘ShinyStan’ app in the default web browser. ‘RStudio’ users also have the option of launching the app in the pop-up Viewer. launch_shinystan is located in package shinystan. Please install and load package shinystan before use. launch_shinystan(object, …) ## Default S3 method: launch_shinystan(object, …, rstudio = getOption(“shinystan.rstudio”))…
R translate_qplot_lattice — EndMemo
R translate_qplot_lattice The major difference between lattice and ggplot2 is that lattice uses a formula based interface. ggplot2 does not because the formula does not generalise well to more complicated situations. translate_qplot_lattice is located in package ggplot2. Please install and load package ggplot2 before use. install.packages(“ggplot2″, repo=”http://cran.r-project.org”, dep=T) library(ggplot2) library(lattice)…
R readRStudioPreference — EndMemo
R readRStudioPreference Reads an internal RStudio IDE preference for the current user. readRStudioPreference is located in package rstudioapi. Please install and load package rstudioapi before use. readRStudioPreference(name, default) name The name of the preference. default The default value of the preference, returned if the preference is not found. install.packages(“rstudioapi”, repo=”http://cran.r-project.org”,…
Installation of DESeq2 package while utilizing free Posit cloud – General
Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager)Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)BiocManager::install(“DESeq2”)‘getOption(“repos”)’ replaces Bioconductor standard repositories,…
R ggplot2-scales-binned — EndMemo
R ggplot2-scales-binned These functions provide the option to use binned palettes along with the ggplot2 package. It goes without saying that it requires ggplot2 to work. ggplot2-scales-binned is located in package paletteer. Please install and load package paletteer before use. scale_colour_paletteer_binned(palette, direction = 1, …) scale_color_paletteer_binned(palette, direction = 1, …)…
DESeq2 installation failures
DESeq2 installation failures 0 Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager) Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2…
Multiple micronutrient deficiencies in early life cause multi-kingdom alterations in the gut microbiome and intrinsic antibiotic resistance genes in mice
Han, X., Ding, S., Lu, J. & Li, Y. Global, regional, and national burdens of common micronutrient deficiencies from 1990 to 2019: a secondary trend analysis based on the Global Burden of Disease 2019 study. eClinicalMedicine 44, 101299 (2022). Article PubMed PubMed Central Google Scholar Bailey, R. L., West, K….
Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient
Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA. 103, 626–631 (2006). Article ADS CAS PubMed PubMed Central Google Scholar Gao, C. & Guo, L. Progress on microbial species diversity, community assembly and functional traits. Biodivers. Sci. 30, 22429 (2022)….
R bioc_install_repos — EndMemo
R bioc_install_repos bioc_version() returns the Bioconductor version for the current or the specified R version. bioc_install_repos is located in package remotes. Please install and load package remotes before use. bioc_version(r_ver = getRversion()) bioc_install_repos(r_ver = getRversion(), bioc_ver = bioc_version(r_ver)) r_ver R version to use. For bioc_install_repos() it is ignored if bioc_ver…
R ggplot2::reexports — EndMemo
R reexports — ggplot2 These objects are imported from other packages. Follow the links below to see their documentation. grid arrow, unit scales alpha . ggplot2::reexports is located in package ggplot2. Please install and load package ggplot2 before use. install.packages(“ggplot2″, repo=”http://cran.r-project.org”, dep=T) library(ggplot2) ggplot(mpg, aes(displ, hwy)) + geom_point(alpha = 0.5,…
How To Install R Packages: Steps For Efficient Integration
Installing R packages is a fundamental skill for every programmer and developer working with R. This guide provides straightforward steps to ensure a smooth installation process. Whether you’re a beginner or an experienced user, these instructions will help you efficiently integrate new packages into your R environment. Understanding R Package…
R geom_spatial_segment — EndMemo
R geom_spatial_segment While the implementation is slightly differrent, this function is intended to behave identically to ggplot2::geom_segment(). Use great_circle = FALSE and detail = NULL if you wish ignore the fact that the earth is round. geom_spatial_segment is located in package ggspatial. Please install and load package ggspatial before use….
python – Docker with Rstudio & conda virtual env – unable to load R packages
I have this dockerfile: # Use the rocker/rstudio image with R version 4.1.2 FROM rocker/rstudio:4.1.2 # Install deps RUN apt-get update && apt-get install -y \ wget \ bzip2 \ bash-completion \ libxml2-dev \ zlib1g-dev \ libxtst6 \ libxt6 \ libhdf5-dev \ libcurl4-openssl-dev \ libssl-dev \ libfontconfig1-dev \ libcairo2-dev \…
Read file with the DSSAT R package – rstudio
Good evening All,I am trying to read experimental file from my system using the DSSAT R package and I get the following error below: I don’t know if there is any expert here that can help me; Here is my reprex: # Load Required Packages library(DSSAT) #> When using the…
R BiocManager::version — EndMemo
R version — BiocManager version() reports the version of Bioconductor appropropriate for this version of R, or the version of Bioconductor requested by the user. BiocManager::version is located in package BiocManager. Please install and load package BiocManager before use. version() ## S3 method for class ‘version_sentinel’ print(x, …) x An…
Recovery of microbial DNA by agar-containing solution from extremely low-biomass specimens including skin
Ethical considerations This study complies with relevant institutional, national, and international guidelines and legislation. The Ethics Committee at the RIKEN Center for Integrative Medical Sciences (H30-4) approved this study, and written informed consent was obtained from all volunteers who provided specimens. Sampling solutions The AgST solution was prepared as follows:…
How To Make A Histogram With Categorical Data In R
Source: Youtube.com Are you looking to create a histogram with categorical data in R? Look no further! In this article, we will explore the step-by-step process of creating a histogram using R programming language, specifically tailored for handling categorical data. Histograms are powerful visualizations that provide insights into the distribution…
r – How do I assign one color to a specific value in ggplot2 function scale_fill_gradient2?
Another option that does not require the addition of a new package. gg <- ggplot(df, aes(x, y, fill = z)) + geom_tile() + scale_fill_gradient2( low = ‘#0017FF’, mid = “white”, high=”#FF2D00″, midpoint = 0, na.value = “grey50” ) To the original plot, overlay another geom_tile with just the cells you…
r – Error: “there is no package called …” and trying to use install.packages to solve it
The R studio I have in my university computer gives me an error when I try to download different packages, whereas when I’m with my laptop in the university server, I don’t get this error. Because of this, I don’t think that there is some kind of a proxy/server problem….
Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques
Victora CG, Bahl R, Barros AJD, França GVA, Horton S, Krasevec J, et al. Breastfeeding in the 21st century: Epidemiology, mechanisms, and lifelong effect. Lancet. 2016;387:475–90. Article PubMed Google Scholar Bardanzellu F, Fanos V, Strigini FAL, Artini PG, Peroni DG. Human breast milk: Exploring the linking ring among emerging components….
Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges
Aizawa M, Yoshimaru H, Saito H, Katsuki T, Kawahara T, Kitamura K et al. (2009) Range‐wide genetic structure in a north‐east Asian spruce (Picea jezoensis) determined using nuclear microsatellite markers. J Biogeogr 36(5):996–1007 Article Google Scholar Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated…
r – How to set Sumatra as default PDF Viewer in RStudio
I want to use Sumatra for viewing Latex Dokuments I make with R because the default R PDF Viewer opens a Sidebar everytime I recompile. So far I installed Sumatra and used the following code as described at search.r-project.org/CRAN/refmans/berryFunctions/html/sumatraInitialize.html sumatraInitialize( path = sub(“pandoc$”, “sumatra”, Sys.getenv(“RSTUDIO_PANDOC”)), roampath = paste0(Sys.getenv(“APPDATA”), “/SumatraPDF”), openfolder…
Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics
Albone, E. S. Mammalian semiochemistry. The investigation of chemical signals between mammals. 2–5 (1984). Wyatt, T. D. Pheromones and Animal Behaviour: Communication by Smell and Taste (Cambridge University Press, 2003). Book Google Scholar Doty, R. L. Odor-guided behavior in mammals. Experientia 42, 257–271 (1986). Article CAS PubMed Google Scholar Brennan,…
Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls
World Health Organization. Facts sheet: suicide. www.who.int/news-room/fact-sheets/detail/suicide. National Institute of Mental Health. Suicide. www.nimh.nih.gov/health/statistics/suicide. Nock MK, Hwang I, Sampson N, Kessler RC, Angermeyer M, Beautrais A, et al. Cross-national analysis of the associations among mental disorders and suicidal behavior: findings from the WHO world mental health surveys. PLoS Med. 2009;6:e1000123….
Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau
Abebe TD, Naz AA, Léon J (2015) Landscape genomics reveal signatures of local adaptation in barley (Hordeum vulgare L.). Front Plant Sci 6:813 Article PubMed PubMed Central Google Scholar Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 Article CAS PubMed …
SparseArray unable to install on Bioc 3.18
SparseArray unable to install on Bioc 3.18 0 @f33be25c Last seen 6 hours ago United States I have been using DESeq2 now for several months and my code has been working just fine for my analysis. However today I was unable to load the DESeq package. It appears the issue…
Getting Started with R-pt1.pdf – Getting Started with R & RStudio Spring 2023 R is a programming environment for statistical computing and graphics. R
Getting Started with R &RStudio (Spring 2023) R is a programming environment for statistical computing and graphics. R is designed to perform operations on vectors and matrices and serves as a data analysis. R also allows for rapid development of new tools (distributed as packages) according to user demand. Any…
Chapter 0 Intro to R – Introduction to R and RStudio The goal of this lab is to introduce you to R
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Nutritional stress compromises mosquito fitness and antiviral immunity, while enhancing dengue virus infection susceptibility
McGraw, J. B. & Caswell, H. Estimation of individual fitness from life-history data. Am. Naturalist 147, 47–64 (1996). Article Google Scholar Price, T. & Schluter, D. On the low heritability of life‐history traits. Evolution 45, 853–861 (1991). Article PubMed Google Scholar Nylin, S. & Gotthard, K. Plasticity in life-history traits….
Package version warning – package ‘extdata’ is not available for Bioconductor version ‘3.17’
Package version warning – package ‘extdata’ is not available for Bioconductor version ‘3.17’ 0 Hi friends how would you deal with a package that is not compatible with my R version? I got this error : Warning message: package ‘extdata’ is not available for Bioconductor version ‘3.17’ A version of…
R package version
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dplyr – installation error package/DESCRIPTION after upgrading R and R studio
Recently I updated R and R studio R version 4.3.2 (2023-10-31 ucrt) — “Eye Holes” Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) RStudio 2023.09.1+494 “Desert Sunflower” Release (cd7011dce393115d3a7c3db799dda4b1c7e88711, 2023-10-16) for windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.09.1+494 Chrome/116.0.5845.190 Electron/26.2.4 Safari/537.36…
RStudio Guide | The GitLab Handbook
RStudio Guide {:toc .toc-list-icons .hidden-md .hidden-lg} {::options parse_block_html=“true” /} What is R? Similar to Python, R is an open-source statistical software that is used to clean and analyze data. It is popular within the data science community and has many packages that make statistical modeling easier for statisticians and data…
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How To Install r-cran-rsqlite on Ubuntu 22.04
In this tutorial we learn how to install r-cran-rsqlite on Ubuntu 22.04. r-cran-rsqlite is Database Interface R driver for SQLite Introduction In this tutorial we learn how to install r-cran-rsqlite on Ubuntu 22.04. What is r-cran-rsqlite r-cran-rsqlite is: This package embeds the SQLite database engine in R and provides an…
How to install or uninstall “r-bioc-genomeinfodb” on Linux Mint 21 “Vanessa” ?
1. Install r-bioc-genomeinfodb package In this section, we are going to explain the necessary steps to install r-bioc-genomeinfodb package: sudo apt install r-bioc-genomeinfodb Copy 2. Uninstall / Remove r-bioc-genomeinfodb package Please follow the guidance below to uninstall r-bioc-genomeinfodb package: sudo apt remove r-bioc-genomeinfodb Copy sudo apt autoclean && sudo apt…
How to install or uninstall “r-bioc-scrnaseq” on Linux Mint 21 “Vanessa” ?
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r – RStudio Posit Migration and package reconnect
(I had not used RStudio for a couple of years and needed to update a few old .Rmd files.) I thus discovered that RStudio had moved to posit. I updated RStudio to the latest version on macos (2023.09.1+494), and made sure I was running the latest R (4.3.1). RStudio still…
CIMB | Free Full-Text | mtDNA Single-Nucleotide Variants Associated with Type 2 Diabetes
1. Introduction Type 2 diabetes (T2D) is the most prevalent metabolic disease and a significant public health concern [1,2], leading to early-onset disability and elevated mortality due to various related complications [3]. Between 1990 and 2017, the global trend in the age-standardized rates of T2D, as measured by the number…
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R: Reverse dependency tools.
R: Reverse dependency tools. revdep {devtools} R Documentation Reverse dependency tools. Description Tools to check and notify maintainers of all CRAN and bioconductor packages that depend on the specified package. Usage revdep(pkg, dependencies = c(“Depends”, “Imports”, “Suggests”, “LinkingTo”), recursive = FALSE, ignore = NULL, bioconductor = FALSE) revdep_maintainers(pkg = “.”)…
r – Issues with rqa in nonlinearTseries version 0.2.12 in RStudio
I am trying to run a simple rqa using nonlinearTseries in R using version 0.2.12 of the library a <- c(1,2,1,2,1,2) a.rqa <- rqa(time.series = a, embedding.dim = 1, time.lag = 1, radius = .1) While I never had any issue with this in the past, I noticed that since…
6.6 Data sources | ggplot2
The USAboundaries package, github.com/ropensci/USAboundaries contains state, county and zip code data for the US. As well as current boundaries, it also has state and county boundaries going back to the 1600s. The tigris package, github.com/walkerke/tigris, makes it easy to access the US Census TIGRIS shapefiles. It contains state, county, zipcode,…
Leishmania genetic exchange is mediated by IgM natural antibodies
Rapaka, R. R. et al. Conserved natural IgM antibodies mediate innate and adaptive immunity against the opportunistic fungus Pneumocystis murina. J. Exp. Med. 207, 2907–2919 (2010). Article CAS PubMed PubMed Central Google Scholar Boehm, T., Iwanami, N. & Hess, I. Evolution of the immune system in the lower vertebrates. Annu….
r – Kaggle scatterplot showing a unique error
I’m using kaggle and today I received an error which I’ve never seen before. library(“tidyverse”) #everything you need for data manipulation library(“ggplot2”) #everything you need for visualization remove.packages(“ggmap”) #stamen is migrating to stadia install.packages(“devtools”) #cran install devtools devtools::install_github(“stadiamaps/ggmap”) #stadia is used for stamen maps stations <- read.csv(“/…/Divvy_Stations_2017_Q3Q4.csv”, na = “”)…