Tag: Rstudio

RStudio Launcher Plugin SDK: rstudio::launcher_plugins::local::LocalPluginApi Class Reference

Launcher Plugin API for the Local Plugin. More… #include <LocalPluginApi.hpp> Inheritance diagram for rstudio::launcher_plugins::local::LocalPluginApi: Detailed Description Launcher Plugin API for the Local Plugin. Constructor & Destructor Documentation ◆ LocalPluginApi() rstudio::launcher_plugins::local::LocalPluginApi::LocalPluginApi ( std::string  in_hostname, std::shared_ptr< comms::AbstractLauncherCommunicator >  in_launcherCommunicator  ) Constructor. Parameters in_hostname The name of the host running this instance of the…

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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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RStudio fails to start up after update to latest version and update of R to 4.2.2 – RStudio IDE

Error Information: Nothing visibleDescription of issue –Updated R and Rstudio after not using it since 2017 (although that version worked)R Works OKRStudio fires up icon then immediately fails with a segmentation fault Attempted steps taken to fix –Deleted all RStudio files and then re-downloaded RStudio . System Information: RStudio Edition:…

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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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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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Senior Data Analyst – IT-Online

A role exists within the Data Science and Analytics team within a global financial services company. Get exposure to working and collaborating with technology teams in South Africa, Rest of Africa, US and India. Key duties include Design and develop robust data workflows accross multiple platforms Drive deep insights from…

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Impact of host age on viral and bacterial communities in a waterbird population

Woolhouse MEJ, Gowtage-Sequeria S. Host range and emerging and reemerging pathogens. Emerg Infect Dis. 2005;11:1842–7. Article  PubMed  PubMed Central  Google Scholar  Allen T, Murray KA, Zambrana-Torrelio C, Morse SS, Rondinini C, Di Marco M, et al. Global hotspots and correlates of emerging zoonotic diseases. Nat Commun. 2017;8:1–10. Article  CAS  Google…

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Single-cell Transcriptomics – SIB Training

Single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression at the single cell level. For example, scRNAseq can help to identify expression patterns that differ between conditions within a cell-type. To generate and analyze scRNAseq data, several methods are available, all with their strengths and weaknesses depending on the…

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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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Bioinformatics Training Project Manager at European Molecular Biology Laboratory (EMBL)

About the team/job Are you passionate about computational training in life sciences and wish to focus your career on the management and coordination of training programs? We are looking for a team member who will coordinate a new multi-organization project (BioNT) funded by the European Commission, embedded in the Data…

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How to add a legend to a ggplot? : RStudio

I want to add a legend for the two lines, either the lines don’t show up or the colors of the graph gets switched up when I try to play with it. Also if I had to reduce the code because I’m mapping a line with points separately, is there…

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r – When debugging in RStudio, how to operate an object in another function in the stack?

Each level of function call comes with its own environment. You can access them with the parent.frame function. Browse[1]> ls() [1] “i3” Browse[1]> ls(parent.frame()) [1] “i2” Browse[1]> ls(parent.frame(2)) [1] “i1” Browse[1]> ls(parent.frame(3)) [1] “f1” “f2” “f3” The last one above is the global environment. Then you can get or change…

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Draw Table in Plot in R (4 Examples) | Barplot, Histogram & Heatmap – Stats Idea

  This article shows several alternatives on how to plot a table object in R programming. The article will consist of the following information: Here’s how to do it!   Creating Example Data Have a look at the example data below: x <- c(letters[1:4], letters[2:4], “d”) # Create example vector…

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Quarto project does not appear even after updating RStudio

RStudio latest version is compatible with macOS version 10.15+ however my OS version is 10.14.6. The latest RStudio version that my OS can support is 2021.09.0 which does not happen to come with Quarto. (Quarto is available in 2022 releases). I upgraded R to version 4.2.1 however, that did not…

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Ggplot Save Plot With Code Examples

Ggplot Save Plot With Code Examples This article will demonstrate via examples how to resolve the Ggplot Save Plot error . ggsave(“filename.png”) We were able to fix the Ggplot Save Plot problem by looking at a number of different examples. How do I save a Ggplot plot? You can either…

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Shiny in Production Conference – RStudio

Shiny is a great way of building interactive web applications without having to have extensive web development knowledge – as long as you know the problem you’re trying to solve, have some ideas of how to display the data, and of course, a bit of R knowledge, you’re good to…

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Installation | _main.knit

Before you start the installation of R, make sure your computer software is up-to-date. To get the most out of R, it is usually best to update to the maximum possible operating system. On a Mac, under the  you can find About This Mac. Then, in the Overview Tab…

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rstudio/tensorflow – bytemeta

TensorFlow for R TensorFlow™ is an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more CPUs…

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r – View() function in RStudio Server opens new tab but does not display data

I am running an Ubuntu 18.04.6 LTS server on Google Cloud Compute Engine. I have downloaded RStudio Server onto my machine and kept getting this message: Warning message: R graphics engine version 15 is not supported by this version of RStudio. The Plots tab will be disabled until a newer…

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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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Window and Pane Management Tricks for RStudio and your OS

Learning the hotkeys for the various programs I use has paid huge dividends in productivity over the years. I can knock out a task in a split second and move on while others are still moving their cursor over the right button. Learning the hotkeys for window management within my…

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Is there a way to force specific dates to display on the x-axis in ggplot? : RStudio

Hello, I’m trying to build a time series of instrument responses against a reference instrument. I pulled the reference instrument data from a SQL server – it’s not been manipulated beyond that. When I try to use the Date_Time to plot that the SQL server spits out, I get the…

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rstudio – How to add eraser to reveal.js presentations in R Markdown

I am a new user of reveal.js presentations in R Studio with no intermediate knowledge of CSS. I followed some blogs and tutorials on the web to produce my first reveal.js presentation in R Studio. I found the chalkboard functionality very useful. However, although I might be able to produce…

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rstudio/package-manager-demo: Demo repository for RStudio Package Manager

GitHub – rstudio/package-manager-demo: Demo repository for RStudio Package Manager This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your…

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rstudio – R Package Check(): “All declared Imports should be used”

I’m writing a small package of functions for myself only (not CRAN; on GitHub, but not public), and developing locally on the computer. Mostly this is me being a newbie at R and learning to write first package. I’m using devtools and after load_all() and check(), I have been getting…

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A*STAR RESEARCH ENTITIES hiring #SGUnitedJobs Bioinformatics Specialist, Lab of Cancer Epigenetic Regulation, GIS in Singapore, Singapore

The Laboratory of Cancer Epigenetic Regulation, helmed by GIS Executive Director Patrick Tan, is seeking a Bioinformatician to join a new multi-institutional effort targeting the genetic basis of cancer to create novel therapies and diagnostics. Led by an award-winning thought leader in the field of Asian gastrointestinal cancer research with…

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Use the tool of your choice (e.g. RStudio, Excel, Python) to generate advanced graphs using given data sets

   Graphs to Produce:Bar Plot: (Use dataset_student_survey_data.csv)x=Smokefill=Exerposition=dodgefacet=Sexx-label=Smokery-label=Countstitle=The Exercise habits of Male and Female students that smokeHistogram: (Use dataset_us_car_price_data.csv)x=Pricefill=Typefacet=Typex-label=Pricey-label=Freqtitle=Car Price Distribution based on Car TypeBox Plot: (Use dataset_production_of_rice_in_india.csv)x=varietiesy=pricefill=bimasfacet=statusx-label=Rice Varietiesx-label=Pricetitle=India Rice Prices based on Varieties, Land Status, and Bimas ProgramScatter Plot: (Use dataset_production_of_rice_in_india.csv)x=pricey=wageshape=bimascol=bimasfacet=statusmethod=lmse=Fx-label=Rice Pricey=Wagetitle=India Rice Prices vs Wage broken down by Land…

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R programming language tutorials – Technical Ripon

Are you learning the R programming language? Want to learn how to do more tasks with R? Check out our Do More With R video tutorials below — most with accompanying text articles and code, almost all under 10 minutes. In the table below you can easily search all tutorials…

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D.E. Analysis: Identifying Differentially-Expressed Genes between Experimental Groups

Username or Email Password Forgot your password? Sign In Cancel by RStudio Sign in Register D.E. Analysis: Identifying Differentially-Expressed Genes between Experimental Groups by HH Last updated about 17 hours ago Hide Comments (–) Share Hide Toolbars × Post on: Twitter Facebook Google+ Or copy & paste this link into…

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Abdullah_DS_Lab03.pdf – CSL-487: Introduction to Data Science Lab BS(CS) – Semester 06 (Spring 2022) Abdullah Abdul Wahid BS(CS) 6B 02-134192-015 Lab

Unformatted text preview: CSL-487: Introduction to Data Science Lab BS(CS) – Semester 06 (Spring 2022) Abdullah Abdul Wahid BS(CS) 6B 02-134192-015 Lab 03: Installation & Introduction to RStudio and Basics 1. Access R Studio Cloud 2. R verses Python Debate 3. R Studio Desktop Installation 4. The R Studio Interface…

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How to normalize biom table from qiime2 to edgeR on Rstudio?

How to normalize biom table from qiime2 to edgeR on Rstudio? 0 Hi, I’m new in this of bioinformatics, I’m making a metagenome analysis of ITS region, then, I want to normalize my data, so i exported a biom table from qiime2 with taxonomic annotations, and then I converted that…

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[Solved] tryCatch not catching error produced by install.packages within RStudio

RStudio does not exectute the normal install.packages but instead does its own thing: look at the code in RStudio: > install.packages function (…) .rs.callAs(name, hook, original, …) <environment: 0x3e4b478> > .rs.callAs function (name, f, …) { withCallingHandlers(tryCatch(f(…), error = function(e) { cat(“Error in “, name, ” : “, e$message, “\n”,…

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R For SEO Part 3: Data Visualisation With GGPlot2 & Wordcloud

[This article was first published on R | Ben Johnston, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don’t. R For SEO Part 3:…

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Please use RSTUDIO!!!!!… | Course Hero

Please use RSTUDIO!!!!! anal=read.csv(‘www.dropbox.com/s/wwls2s6rqnodpe5/anal painRed.txt?dl=1′,header=T,sep=’,’) attach(anal) Image transcription text 5) 3. Arthritis is a very commonly occurring amiction. It is a major cause of lost work time and often results in serious disability. Of the many types of arthritis, the most common type is osteoarthritis. This condition is frequently due…

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r – How to scatterplot in RStudio

I am trying to create a scatterplot in rstudio with my data. I am new to rstudio and having a lot of time understanding. The code I have found says plot(). This is what I used: plot(pa2_wti2$ï..Approving, pa2_wti2$ï..Price) Even when I tried a single it didn’t give me a scatter…

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Foundations of Git connectivity with RStudio

Good ay all, R-Ladies has another educational webinar on how to use Git. Gracielle Higino will cover foundations of version control, useful git commands and connections with RStudio. Saturday, April 30, 2022 10:00 AM to 11:30 AM SAST passcode:   000111 Gracielle is an open science enthusiast and advocate. Her research…

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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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Please solve the question in Rstudio codes with

Transcribed image text: Please solve the question in Rstudio codes with result. DO NOT solve on paper 1 1 3. (2 points) In homework 1, we looked at the bladder1 data from the survival package. > library (survival); head (bladderi, 10) id treatment number size recur start stop status rtumor…

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RStudio AI Weblog: pins 0.4: Versioning

A new version of pins is available on CRAN today, which adds support for versioning your datasets and DigitalOcean Spaces boards! As a quick recap, the pins package allows you to cache, discover and share resources. You can use pins in a wide range of situations, from downloading a dataset…

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Need help from a math quant. Must know R/Rstudio – Freelance Job in AI & Machine Learning – Less than 30 hrs/week – undefined

Part 1) Need help analyzing data and coming up with the most profitable portfolio possible Part 2) I need to get some simulations running as fast as possible. I have the code completely finished so I just need suggestions on how to make it better. Video available if needed. I…

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R package with CRAN and Bioconductor dependencies

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

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Download RStudio 2022.02.1+461 (Mac) – Download Free – Heaven32

Download Free RStudio 2022.02.1+461 (Mac) – Download studio is an efficient and versatile user interface for the R programming language and runs on macOS, Linux and Windows. R is a free and open source programming language and environment for statistical computing and graphics that provides many graphics and statistical techniques….

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“Rprofile”to use rstudio on MAC

. rprofile againI received a comment at A recent post and taught me how to send command from R console to terminal using system functions.Used.As described above, the following is described in the console of the upper left corner of rstudio. library(stats) library(tidyverse) library(ggplot2) library(GGally) library(patchwork) library(lubridate) library(dplyr) We named…

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Bioconductor installation problems

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

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Analysis of differential gene expression of bulk RNA-seq data using “DESeq2” in RStudio. – Yale Library Study Spaces Scheduling

RNA-Seq is a high-throughput sequencing method used for unbiased detection and quantification of messenger RNA molecules, allowing the identification of genes and pathways underlying normal and pathological conditions. RNA-seq sequencing services are increasingly affordable which has led to the proliferation of published data available in public repositories accessible for everyone’s…

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Running rstudio (but not R alone) inside of a conda environment complains about finding Rccp.so

I find that when I try to load some packages in a conda environement, when using rstudio (but not when I’m using R directly), I get an error message about a missing Rcpp.so file. I activate my conda environment (which is running R version 4.1), open RStudio (which I installed…

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r – Programmatically close Data Viewer tabs in RStudio

I wanted to make a script that closes all Data Viewer tabs in RStudio (those invoked by clicking on a data object in the Environment pane, or by calling utils::View()) but keeps all the “usual” document tabs.First, I found rstudioapi::documentClose() function – not sure if it works for Data Viewer…

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Error on Rstudio cloud when installing DESeq2 package : rprogramming

Hi! I am using the free account on R studio cloud. And I am getting this error: * installing *source* package ‘DESeq2’ … ** using staged installation ** libs g++ -std=gnu++14 -I”/opt/R/4.1.2/lib/R/include” -DNDEBUG -I’/cloud/lib/x86_64-pc-linux-gnu-library/4.1/Rcpp/include’ -I’/cloud/lib/x86_64-pc-linux-gnu-library/4.1/RcppArmadillo/include’ -I/usr/local/include -fpic -g -O2 -c DESeq2.cpp -o DESeq2.o g++: fatal error: Killed signal terminated program…

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New to R and conflicted about my progress so far : RStudio

So I am a master’s graduate with zero background in programming (dropped computer science back in 8th grade) but I have done mathematics(calculus, differential equations, probability, statistics etc) in one form or another my entire life. Being stuck at home, I felt like learning a programming language and I was…

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Bioconductor Package Installation

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

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Error installing package in RStudio – Software & Applications

Guys, I am trying to install this package on RStudio. I tried to install it on a windows virtual machine and it worked. I thought you guys could know what is happening and how to fix it. When I try to install the following happens: > install.packages(“minqa”) #This package is…

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How To Plot The Log Of Somethin Gin Rstudio?

R’s log() function returns the logarithm of a value and is formatted as log(value, base). You can also use the logy() function to do a log in R. The natural logarithm of the value is the default output of this function. How Do I Create A Log In R? set…

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[Solved] 1.Import HBAT200data into RStudio 2. Build an appropriate…

1. Import HBAT200 data into RStudio 2. Build an appropriate regression model that will explain X22, “Current purchase/Usage Level” (Please note that X19-X23 are outcome variable, so do NOT use them as your independent variables) 3. Check model assumptions 4. Interpret the model and identify the factors that influence Current purchase/Usage Level…

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Library series workshop offering data services

Data Services Workshops are designed to provide faculty and students with training in data management, data visualization and analysis software platforms, and finding data resources. To register for these workshops, follow the links attached to each event. R and RStudio Special Topic: Scrapping TwitterThis workshop will introduce participants to using…

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rstudio::conf(2022) is open for registration!

rstudio::conf, the conference for all things R and RStudio, will take place July 25-28 in National Harbor, DC! As usual, we’ll have two days of workshops followed by two days of talks. If you’ve attended before and already know you want to attend, register now! Otherwise, read on to learn…

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How do I resolve Rd warning “missing file link” when building packages in RStudio?

After building a simple test package to isolate this issue, I receive the following warning when I run Rcmd.exe INSTALL –nomultiarch –with-keep.source simpleTest: * installing to library ‘C:/Users/user/Documents/R-dev’ * installing *source* package ‘simpleTest’ … ** R ** preparing package for lazy loading ** help *** installing help indices converting help…

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Workflow Platforms for Systems Genetics

Workflow Platforms for Systems Genetics eQTL Platforms eQTL Viewer Mouse Genome Informatics: Phenotypes, Alleles & Disease Models PhenoGen Informatics (CO U) eXtensible Genotype And Phenotype platform (XGAP) MOLGENIS & MetaNetwork, Swertz & Jansen, U Groningen Weighted Gene Co-expression Network Analysis (WGCNA), Horvath, UCLA iPlant Sage Bionetworks Repository: Synapse GenomeSpace Institute…

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Adding headings and subheadings to existing code – RStudio IDE

When the code for a particular project starts to get long, I often wish that there was an easy way to insert differently formatted headings for the major and minor sections, with larger print and perhaps bolding or a different typeface, just to help me navigate my own code. So…

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Free PDF Download – Mastering RStudio

Mastering RStudio – Develop, Communicate, and Collaborate with R will help you to solve real-world data problems. It begins by guiding you through the installation of RStudio and explaining the user interface step by step. From there, the next logical step is to use this knowledge to improve your data…

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Research Assistant, CSCB,LWK job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The SingHealth Duke-NUS Genomic Medicine Centre was established by SingHealth and Duke-NUS Medical School to advance the delivery of genomic medicine across the SingHealth Duke-NUS Academic Medical Centre (AMC). The Centre will bring together expertise from the various SingHealth institutions and Duke-NUS to leverage on advanced genomic technologies…

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Best portable device for RStudio ? : RStudio

That depends on what kind of work you want to do. Until recently, I used Acer Swift 3 SF314-54 as my laptop and it was enough for most things, except for big Bayesian models (which I computed on a remote server). It should cost circa 600-700$. If you want to…

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adding a prefix to file names? : RStudio

Hello there, I am currently struggling with changing the names of certain files and would appreciate some direction. I have pulled all the files I would like to change, into a vector like so. [1]”Fruit/Red/Berries/Strawberry.jpg” [2]”Fruit/Red/Apples.jpg” [3]”Fruit/Blue/Berries/Blueberry.jpg” etc. I have hundreds of these and would like to add a prefix…

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Unable to install RStudio on Mac OSX 10.10

I was able to solve this problem by deleting all R/RStudio resources which remained from installing them manually from .dmg: Uninstall CRAN R GUI app (drag it into the trash) Uninstall RStudio app (drag it into the trash) From Terminal: $ rm -rf ~/.rstudio-desktop/ $ rm -rf /Library/Frameworks/R.framework /Applications/R.app /usr/bin/R…

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Download, unzip, and share a large size file in R – General

I think reproducibility is challenging to achieve for students/researchers who have limited access to bigger data storage, and a very important topic to talk about to get ready to jump into the real-world work setting.So I wanted to create a thread here to ask questions. Plus, I asked for help…

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Decision Tree Shiny App : RStudio

This would be a fairly simple Shiny app to build. Your best bet to start is with the Shiny documentation here, particularly the get started and gallery sections. You could try the book Mastering Shiny but that’s probably overkill for such a simple app. Note, to share this with your…

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r – Akima function ‘bilinear’ is only returning zeros when making interpolations in RStudio

I’m trying to interpolate data from ERA5 Interim to a finer resolution (from 0.1° to 0.05°). I’m using the bilinear function from the akima package in Rstudio to do so, but whenever I try to compute it I only get zeros. What might be the reason behind this? As a…

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How to order sample names with the phyloseq object for heatmap

Hello!I am new to the Rstudio!I can’t find a tutorial, or instructions for ordering our samples in the heatmapI have created the phyloseq object with the next scripts physeq<-qza_to_phyloseq(features=”file path/rarefied_table.qza”,metadata=”file path/Metadata.tsv”)taxonomy = read.csv(“file path/taxonomy.csv”,sep=”,”,row.names=1)taxonomy =as.matrix(taxonomy)TAX = tax_table(taxonomy)data_full<-merge_phyloseq(physeq,TAX) then I use ph = tax_glom(data_full, taxrank=’Genus’,NArm=FALSE)TOP = names(sort(taxa_sums(ph), TRUE)[1:20])TOPp = prune_taxa(TOP, ph)plot_heatmap(TOPp,…

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bioconductor – Trouble installing Rhtslib in R/R studio

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

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Bioconductor on Microsoft Azure – Microsoft Tech Community

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

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Importing matplotlib.pyplot in Rstudio using reticulate

I had similar issues. I did following and it solved. Before that I would like to refer you in following threads from where I got the solution… Qt platform plugin issue Rstudio PyQt5 – Failed to load platform plugin “windows”. Available platforms are: windows, minimal Here is what you have…

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RStudio is slow when loading a project / package in development

I have recently experienced a serious problem with Rstudio when developing a package. Whenever, I open an existing project with Rstudio where versions are controlled with Git, it takes so long for it to respond to any command. It is also impossible to type something in the console (e.g. 1+1)…

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r – How to change the resolution of animated plots (gif) in RStudio Viewer?

I guess those plots shown in the gganimate article were created on a Linux platform. gganimate by default uses the ‘png’ device for rendering the single frames. png() on windows however by default uses the Windows GDI which is not available on Linux (cairographics is used). This is (probably) why…

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r – Importing huge SAS database to Rstudio

I have a huge dataset in SAS (about 14 gb) that I am trying to import to R-studio for some analysis. However, nothing is working for importation. I tried ‘haven’, ‘sas7bdat’, ‘foreign’ but nothing. I converted the file to csv (became about 7gb) and tried read.csv, fread..but nothing again. R-studio…

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Python – run indented code through keyboard shortcuts in spyder as in rstudio ( Python, R )

Problem : ( Scroll to solution ) I would like to be able to run an indented block of code in python in the same way I do in R. In particular, if in RStudio I have the following indented block of code: print(seq(from = 1, to = 10, by…

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r – I can’t load libraries into Rstudio

Summary of problem: I install packages successfully but my libraries will not load. This problem has only happened recently. What steps have I taken?: I uninstalled and reinstalled Rstudio. I uninstalled and reinstalled the packages I want while setting dependencies = TRUE. Whenever I try to load the library of…

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Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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R and sra toolkit – odd system() behavior ( R, System )

Problem : ( Scroll to solution ) In order to extract some fastq data from NCBI’s sequence read archive I’ve downloaded and installed the sra toolkit for Windows. In order to test if it is setup correctly, I opened cmd, navigated to the directory and typed in the command fasterq-dump…

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r – RStudio session aborts when I run gRbase::stepwise function (undirected graphs)

I’m doing an R project on RStudio (RStudio 2021.09.1+372 “Ghost Orchid” Release for Windows), (R version 4.1.2). I’m working on Windows 10 x64. I want to create an Undirected Graph from a dataset: library(gRbase) library(gRim) library(gRain) data(BodyFat) BodyFat <- BodyFat[-c(31,42,48,76,86,96,159,169,175,182,206),] BodyFat$Age <- sqrt(BodyFat$Age) BodyFat$Weight <- sqrt(BodyFat$Weight) names(BodyFat)[names(BodyFat) == ‘BodyFat’] <-…

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Having problem with RSQLite : RStudio

Hi, I’m trying to learn how to use RSQLite but I’m already having a problem, wondered if anyone knows how to fix it. I have a pre-existing database (.data) file which does not have attribute names and I am trying to create a SQLite database with a table defined with…

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3 RStudio Professional Database Drivers

The RStudio Pro Database Drivers are installed on-demand by the RStudio IDE. Doing so requires internet connectivity. To test this, start RStudio and invoke the New Connection dialog from the Connections pane. The New Connection dialog shows the available database drivers. Select one, such as MySQL. RStudio first offers to…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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Software Engineer – RStudio

In 2011, Tim worked in software development while obtaining his computer science degree. He has worked in this field ever since. Over the years, he focused on server side development and cloud infrastructure. Tim loves the satisfaction of learning new things and building great software. After spending several years in…

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Anne Carome – Manager, Events – RStudio Inc

RStudio Inc 250 Northern Ave., Boston, Massachusetts, 2210, United States Last updated 5 days ago RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. RStudio,…

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summary-statistics – Github Help

0 1 0 summary-statistics,Fictional company AutosRUs’ newest prototype, the MechaCar, is suffering from production troubles that are blocking the manufacturing team’s progress. AutosRUs’ senior management enlisted assistance from the data analytics team to review the production data for insights that may help the manufacturing team overcome their production issues. User:…

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r – Changing chr to datetime on RStudio

Want to improve this question? Update the question so it’s on-topic for Cross Validated. Closed 4 hours ago. I would like to change a chr column in my dataframe to a datetime column. Date Value 1 01/7/20 13:05 100 2 01/7/20 13:15 102 3…

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How To Install RStudio IDE on Fedora 35

In this tutorial, we will show you how to install RStudio IDE on Fedora 35. For those of you who didn’t know, RStudio provides free and open-source tools for R and enterprise-ready professional software for data science teams to develop and share their work at scale. RStudio makes it easier…

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R Running Slowly on VM – RStudio IDE

Hi, I’m trying to run R on a virtual machine through work, but it is running very slowly. I was running code on a physical machine, but I needed more RAM than was available. I was able to have a new virtual machine created for me with more RAM, which…

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docx files fail to open in RStudio on Debian (at least 11) – Java rstudio

System details RStudio Edition : Dektop RStudio Version : 1.4.1717 and 2021.09.0+350 OS Version : Debian 11 R Version : 4.0.4 Steps to reproduce the problem Knit an R Markdown file to Word format. The file should be created. However, it’s not automatically opened. Click on the file in the…

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Characterization of Blood- Based Molecular Profiling in Pancreatic Adenocarcinoma

Introduction Most cases of pancreatic adenocarcinoma (PDAC) are diagnosed in the metastatic or locally advanced stage. It is the fourth leading cause of cancer death in the United States,1,2 with a 5-year overall survival (OS) around 10% in this country2 despite years of research and therapeutic development. For those patients…

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sequence alignment – Help with MinION sequencing data species identification

Hi I’m new to bioinformatics and have just completed my first run on the MinION (long read sequencing Oxford Nanopore Technologies). I was hoping someone could direct me towards R packages, workflow, tutorials or guides that will help me identify species that are present in my sample mainly for fungi…

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Compiling *.Rnw files with knitr –without Rstudio

Instead of going through Rstudio, you can use the functions in the knitr package directly. There are some options you can tweak, but to get started, all you have to do is call the knit() function on your .Rnw file: library(knitr) knit(‘my_input.Rnw’) If you’re missing some of Rstudio’s features, it’s…

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x-session – RStudio

blog Shiny Apps from Concept to Production – An RStudio Community X-Session with Appsilon Curtis Kephart | July 27, 2021 | Ready to take your Shiny development skills to the next level? This RStudio Community X-Session connects you with the Shiny experts at Appsilon. The two-hour workshop covers development workflows,…

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Excelraise, LLC DataBase Programmer / DataBase Analyst (ETL / Salesforce CRM / RStudio / SQL) 100% Remote

Job Detail Job Description Excelraise, LLC is a rapidly growing full service IT solutions integrator and talent management company headquartered in Denver, CO. Our valued client*s includes fortune 500 companies, Government Agencies. Currently we are looking for a qualified individual to work as a DataBase Programmer / DataBase Analyst (ETL…

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Which R and RStudio version to install for Windows 32 bit?

The last version of RStudio to support a 32-bit OS was 1.1.463. You can download it from here (scroll down until you find it). You should be able to install the latest release of R from here, just make sure that you install the 32-bit version. From experience, R/Rstudio 1.1.463…

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RStudio AI Weblog: Picture segmentation with U-Internet

Certain, it’s good when I’ve an image of some object, and a neural community can inform me what sort of object that’s. Extra realistically, there is perhaps a number of salient objects in that image, and it tells me what they’re, and the place they’re. The latter process (referred to…

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How to Clear Console in R and RStudio

Everyone loves a clean working environment and it helps to increase productivity. This works the most especially for programmers and those that make regular use of the R or Rstudio consoles on their computers. However, a lot of lines and commands in the console can sometimes hinder productivity which is…

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RStudio AI Weblog: Introducing: The RStudio AI Weblog

Why the brand new title, RStudio AI Weblog? There’s a easy motive. The earlier title, “TensorFlow for R Weblog”, was an excellent match for the content material we lined to date: technical or utilized features of performing deep studying with TensorFlow and Keras. But, our crew (the Multiverse Group) is…

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Draw Cumulative Histogram in R (Example)

  In this R tutorial you’ll learn how to draw the cumulative sum of a vector in a histogram. Table of contents: Here’s how to do it!   Example Data The following data is used as basement for this R programming language tutorial: set.seed(258967) # Create example data data <-…

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