Tag: dplyr

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…

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Deleting a column from data frame and then running DESeq2

Forgive me if this post is messy, I’m new to this! I’m analyzing RNA Seq data and found that one of my samples is an outlier (sample AV17). I’m trying to exclude it from my analysis, but whenever I do, using this code: dds = subset(countData, select = -c(AV17) ),…

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Adding New Inputs to a Chart of Monthly Operating Profits – tidyverse

I pulled some data from Fama French web site on operating data by month…here is my code that works (below). I have 7 columns of data, with headers, including Date. I have successfully graphed one column data, but I would like to add several of the other columns of data…

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ggplot2 – Overlaying a background with hexagonal points on ggplot r

I’m desperately trying to add inventory data (available online, as in this reproducible example below) in ggplot with a background of France, so that I can visualize the areas where there are no records of my species. However, I want to do it with hexagons and not points. So, I…

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r – Changing Title of Legend in ggplot2 Creates a Second Legend?

I am pretty new to R/working with data and am trying to change the title of the legend in a visualization I made. I have tried using fill= in the labels() function I have but it adds another legend for some reason. I have looked around for a solution and…

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Complete Tutorial Guide / AvaxHome

Parallel Computing With R & Rstudio: Complete Tutorial GuidePublished 12/2023MP4 | Video: h264, 1920×1080 | Audio: AAC, 44.1 KHzLanguage: English | Size: 1.30 GB | Duration: 1h 30m R Programming, RStudio, Parallel Computing, Multicore, Data Science, Speed Optimization What you’ll learn Understand core parallel computing concepts. Explore essential R packages…

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Update to (git-version 2.0.1 revision commit).

* gnu/packages/bioinformatics.scm (r-sccustomize): Update to (git-version 2.0.1 revision commit). Change-Id: I4e4b499a658eaed0396263d1d9fd277a541a13d9 — gnu/packages/bioinformatics.scm | 87 ++++++++++++++++—————– 1 file changed, 43 insertions(+), 44 deletions(-) Toggle diff (108 lines) diff –git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2546454acd..3e7b99ee61 100644 — a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10245,55 +10245,54 @@ (define-public r-presto (license license:gpl3)))) (define-public r-sccustomize – (let…

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No genes mapped in clusterprofiler gseGO

Hello! I’m having issues generating an adequate geneList for running gseGO in clusterProfiler, using keytype = “GO” Similar issues have been described here: No gene mapped gseGO code is: gse <- gseGO(geneList = gene_List, ont = “ALL”, #ont one of “BP”, “MF”, “CC” or “ALL” OrgDb = OrgDb, minGSSize =…

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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…

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Delete or Drop rows in R with conditions

Drop rows in R with conditions can be done with the help of subset () function. Let’s see how to delete or drop rows with multiple conditions in R with an example.  Drop rows with missing and null values is accomplished using omit(), complete.cases() and slice() function. Drop rows by…

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Error in calculating inter-individual divergence / spread

Hi all I am currently facing an issue while working with the microbiome package in R and would greatly appreciate your insights. > b.lgg <- divergence(subset_samples(physeq, Description == “Stool_controls”), + apply(abundances(subset_samples(physeq, Description == “Stool_controls”)), 1, median)) > b.pla <- divergence(subset_samples(physeq, Description == “Stool_samples”), + apply(abundances(subset_samples(physeq, Description == “Stool_samples”)), 1, median))…

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Bioconductor – chimeraviz

DOI: 10.18129/B9.bioc.chimeraviz     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see chimeraviz. Visualization tools for gene fusions Bioconductor version: 3.12 chimeraviz manages data from fusion gene finders and provides useful visualization tools. Author: Stian Lågstad [aut, cre], Sen Zhao [ctb], Andreas M….

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facet grid – ggplot facet_grid: need lines between outside strip placement and panels

I am using facet_grid to create a plot with one column and multiple rows, with an outside strip placement to the left of the y-axis tick mark labels. I would like to enclose the y-axis tick mark labels such that each facet strip label is cleanly attached to its associated…

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A Guide for Data Science Beginners

Data science and programming have become increasingly important in today’s world, and two languages have emerged as the top contenders: R and Python. Many newcomers to the field often find themselves wondering which language is more challenging to learn and master. Let’s take a closer look at the complexities of…

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A Battle of Statistical Titans

A fierce debate has been brewing in the data science community: which programming language reigns supreme for statistical analysis? Python and R have emerged as the heavyweight contenders, each with its own dedicated following. While they share similarities in their data manipulation and visualization capabilities, the question remains: can Python…

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Bioconductor – clusterProfiler

DOI: 10.18129/B9.bioc.clusterProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler. statistical analysis and visualization of functional profiles for genes and gene clusters Bioconductor version: 3.12 This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene…

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Google Data Analytics-Study Case 1:RStudio & Tableu | by Assyifa Nur Aziza | Dec, 2023

Recently, I completed Google Data Analytics Professional by Coursera. The course is challenging and exciting at the same time. However, it is worth studying. The course consists of 8 chapters, and at the end of the chapter, there are several case studies to solve. This article will consist of a…

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Wrangling And Analyzing Data In RStudio

Article Summary Box Efficient data preparation in RStudio hinges on automated data cleaning techniques, significantly reducing manual errors and streamlining the initial stages of analysis. Vectorized operations and the apply() family functions in RStudio dramatically enhance data manipulation efficiency, especially for large datasets. Utilizing multiple linear regression and PCA in…

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Bioconductor – QTLExperiment (development version)

DOI: 10.18129/B9.bioc.QTLExperiment   This is the development version of QTLExperiment; for the stable release version, see QTLExperiment. S4 classes for QTL summary statistics and metadata Bioconductor version: Development (3.19) QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It…

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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…

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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…

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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…

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Writing R Scripts In RStudio: A Step-By-Step Approach

Article Summary Box Mastering the RStudio interface goes beyond basic navigation, involving strategic use of panes and shortcuts to streamline the coding process. Effective script organization significantly impacts readability and maintenance, emphasizing the role of modular structuring and clear documentation. In debugging and error handling, advanced techniques like conditional breakpoints…

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Data forecasting in R Studio – General

Hi Everyone, I am trying to do forecasting in R Studio however, I ended up getting errors. Could someone help me with the forecasting model in R Studio? Below is the R code: install.packages(“DBI”)install.packages(“odbc”)install.packages(“tidyverse”)install.packages(“forecast”) library(DBI)library(odbc)library(tidyverse)library(forecast) con <- dbConnect(odbc(),driver = “SQL Server”,server = “PRD1”,database = “DUMMY”,trusted_connection = “yes”) query <- “SELECT…

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r – Adjust plot.background margin in ggplot

My plot background is much larger than the plot and I can’t figure out how to reduce it. I have hacked a way to bring the title closer to the plot, but there is still a large space below the plot. This causes issues when I use cowplot to place…

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database – R Studio – Bagging throws “subscript out of bounds” error

I am trying to create a classification model that predicts the variable ‘sex’ in my dataset. When I try to run the line “abalone.bagging <- bagging(formula = M~., data = abalone.train)”, it throws this error: Error in [<-(*tmp*, , i, value = matrix(as.numeric(pred == levels(vardep)[i]), : subscript out of bounds…

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How to use RStudio

Article Summary Box Customizing the RStudio Environment significantly boosts productivity, with options like project-specific settings and theme personalization enhancing the user experience. Advanced ggplot2 Techniques in data visualization offer a blend of aesthetics and functionality, enabling the creation of visually striking and informative plots. Efficient Data Management strategies in RStudio,…

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removeBatchEffect with non-linear model fit

removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…

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r – Preserving box plot whiskers when mixing box and violin plots in {ggplot2}

Preamble Let’s say I have a function that allows users to create a boxviolin plot where box and violin plots are superposed. library(ggplot2) df <- dplyr::filter(mpg, class %in% c(“compact”, “midsize”)) p1 <- ggplot(df, aes(class, hwy)) + geom_violin() + geom_boxplot() p1 I also want to allow users to remove the violin…

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ggplot2 – Error knitting from R Markdown ggplot – unexpected special character that doesn’t exist

I’m getting an error when I try to knit my .Rmd file. The code itself runs fine inside the file; the error only occurs when I try to knit. Quitting from lines 103-118 [unnamed-chunk-4] (Lab-14.Rmd) Warning messages: 1: In eng_r(options) : Failed to tidy R code in chunk ‘unnamed-chunk-2’. Reason:…

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r – GGplot graph changes when used with plotly

I’m trying to make my GGplot interactive with plotly but the graphs change completely given the following code. Any advice on where I may be going wrong is highly appreciated. I have tried to follow some previous posts on this topic but nothing seems to be helping. I have attached…

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Solved: R-script ggplots broken in Services

We are having the same problem.  The reports were working just fine in the services then all of a sudden our R visuals would not show in the PowerBI service.  They continue to function on the desktop.  Here is the error we are receiving.   Script Runtime Error — Attaching…

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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…

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Interaction terms in DESeq2

Hi, I am hoping this isn’t a stupid question as I am really lost here. I have extensively read the manual and other forum posts but am struggling to find a solution. I am using DESeq2 to analyse my data set but running into problems with an interaction term in…

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Bioconductor – pgxRpi (development version)

DOI: 10.18129/B9.bioc.pgxRpi   This is the development version of pgxRpi; to use it, please install the devel version of Bioconductor. R wrapper for Progenetix Bioconductor version: Development (3.19) The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a…

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ggplot2 – Finding the middle of the y axis in a ggplot with facets and free scales

I have a facetted density plot with free scales, to which I would like to overlay a geom_pointrange to represent the summary of the distribution. However, I’d like this point to be fixed in the middle of my y axis for each facets (with the x varying according to the…

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scRNA data analysis , how to compare pattern in multiple samples

Hello Everyone . I am new to single cell data . in this path G:\RNA\sc\scdata I have 3 files Sample5D_barcodes Sample5D_features Sample5D_matrix.mtx I want to see cell clusters and differentially expressed genes for this single cell sample. I am running this command in R install.packages(c(“Seurat”, “ggplot2”, “Matrix”, “dplyr”)) library(Seurat) library(ggplot2)…

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ScRNAseq analysis scran :: quickcluster Error

ScRNAseq analysis scran :: quickcluster Error 1 @d4a334e3 Last seen 15 hours ago Germany Hello! I am having an error while doing normalization for my scRNAseq data, I would appreciate the help of anyone who countered the same problem the error is during quickcluster command as follow: clust <- quickCluster(sce)…

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Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP

ISCA fabrication VeroGray polymer was used to create 3D-printed moulds on an Objet30 3D printer (Stratasys), using previously described protocols32. Each ISCA consisted of 25 wells arranged in a 5 × 5 array. Each 110 µL well possessed a 800-μm-diameter port that connected the inside of the well with the surrounding seawater and…

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How to choose only two years in R using lubridate (not including years in between)

I am using RStudio and a semi-large data set in which I want to only select the years 2016 and 2023 in the data set in the column observation_date. I tried using the lubridate to do this. However, I have only found how to select in between the two years…

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ggplot2 – r time range plot before and after

This is a good use case for a dumbbell plot using the ggalt package: library(ggplot2) #install.packages(“ggalt”) library(ggalt) # For geom_dumbbell library(dplyr) library(tidyr) data %>% separate(Year, into = c(“StartYear”, “EndYear”), convert = TRUE) %>% mutate(Color = ifelse(StartYear < 2016 & EndYear > 2016, “overlap”, ifelse(EndYear <= 2016, “before”, “after”))) %>% ggplot(aes(x…

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How to Use stat_summary() Function in ggplot2

You can use the stat_summary() function in ggplot2 to create visualizations that display summary metrics of specific variables in a data frame. The following examples show how to use the stat_summary() function in practice with the following data frame in R: #create data frame df = data.frame(team=rep(c(‘A’, ‘B’, ‘C’), each=4), …

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Bioconductor – octad (development version)

DOI: 10.18129/B9.bioc.octad   This is the development version of octad; for the stable release version, see octad. Open Cancer TherApeutic Discovery (OCTAD) Bioconductor version: Development (3.19) OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene…

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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…

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How to manually pick colors of geom_line() in ggplot2 based on the slope’s sign? R

(apologies in advance, I don’t know how to make the output show up here…) I’m trying to create a line graph where the lines are colored red if positive slope or green if negative slope. I found this answer which was very helpful, but I’d like to change the colors…

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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…

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Should we learn both R and Python?

Title: The Power Duo: Embracing the Synergy of R and Python in Data Science Introduction:In the realm of data science, the debate over which programming language to learn, R or Python, has been a topic of discussion for years. While some argue for specialization in one language, others advocate for…

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r – Copying host libraries in the image build from my Dockerfile

Is it possible to copy a local .Rprofile file from the host, during the building of the image with a Dockerfile ? I would like to copy this .Rprofile file in the following directory : /home/rstudio I had my Dockerfile as follow : FROM rocker/rstudio:4.2.0 as builder ARG bioc_ver=3.16 RUN…

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KCouper/Liverpool K-means RNAseq Analysis November 2020

R3 VAR14 vs RBC no TNF k-means q0.05 1. Genelist Selection groupsName<-“R3_VAR14_kmeans_q0.05” countsTable<-read.delim(“RNAseq2019July_5.txt”, header = TRUE, sep = “\t”,check.names=FALSE,row.names=1) head(countsTable) AllGeneNames<-countsTable$Gene_Symbol #head(AllGeneNames) tempA<-countsTable topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_0h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_0h))####find indexes listA<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_2h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_2h))####find indexes listB<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_6h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_6h))####find indexes listC<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_20h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_20h))####find indexes listD<-tempA[ topDEgenes,…

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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,…

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Urgently need Data Scientist_Chennai Job in Deuglo Infosystem Private Limited at Chennai,Other Tamil Nadu -Job Description #13418877

Job Details Job Title: Data Scientist (R, ETL, IOT, RStudio Server, Shiny Server, Mariadb MySQL) Job Overview We are seeking a highly skilled and motivated data scientist with expertise in R programming and experience in managing ETL pipelines from sensor data, RStudio Server, Shiny Server, and Mariadb RDBMS. The ideal…

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Solved If you have decided to use RStudio:Model 1Run a logit

If you have decided to use RStudio: Model 1 Run a logit model and use being a member of network and find out its impact on hospital ownership and hospital beds? (Model 1) Model 2 Now, include hospital income and report the Coeff.? (Model 2) Model 3 Now, include the…

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Comparing 3 Data Sets using DeSeq and Heatmaps

Hi all, I am new to bioinformatics analysis, so I’d appreciate if someone could check my code for the goal I am trying to achieve. I have 3 samples – Wild Type (WT) FoxP3-TCF-HEB (I have 3 replicates of this) TCFKO I have defined these in the sample information csv…

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r – How can I turn off scientific notation in ggplot2::cut_interval()?

Usually options(scipen = 999) turns off scientific notation. But I can’t get it to work in ggplot2::cut_interval(). How can I do that? library(dplyr) library(ggplot2) options(scipen = 999) # disable scientific notation # build example data frame df <- data.frame( number = c(10047,439,111,10385,5,10384,10460) ) # create grouping variable df %>% mutate(…

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rstudio – How do I classify universities per state in R?

There are two different aspects of this question, including: Where do I find information about U.S. colleges and universities that includes the state in which the colleges are located? Given a source of information, how do I use R to create a data frame that includes the college name and…

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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…

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How To Input Data In R

Source: Ytimg.com When it comes to analyzing and visualizing data, R is one of the most powerful programming languages available. With its extensive packages and functions, R provides a wide range of tools for data manipulation and statistical analysis. However, before you can leverage the capabilities of R, you need…

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r – how to create age groups in rstudio with dplyr

how to create age groups in rstudio with dplyr, before 1 year, between 1 and 4 years, between 15 and 29 years, between 30 and 59 years and after 59 years. After that, I have the mortality rate variable and I want to know what the mortality rate is by…

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r – Adjusting grid lines and plotting significance stars in GGplot2

A discrete scale has no minor breaks. Hence, panel.grid.minor will have no effect. But you could easily fake minor grid lines using geom_h/vline. For your siginifance stars you could use a geom_text. Note: I dropped the coord_flip and switched the role of x and y. library(ggplot2) library(dplyr, warn = FALSE)…

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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…

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Sorting column that is a character type but has numbers in it. – General

Your values in col1 look like they were generated by the cut() function or some similar function. If so, they should be factor levels to begin with and they will sort correctly using the arrange() function. Here is an example of that. library(dplyr) my_dataframe <- data.frame(A= c(5,8,1,4,99999,8,2,10,3,3,7,8,2), Count = 1)…

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Rstudio crashes just before producing a brms model – General

Hello, I am trying to run a brms model with 20000 iterations. After many hours of simulations, and just before being done, Rstudio crashes without any warning. The model compiles successfully with 1000 iterations and, sometimes, with 10000 iterations but several attempts to run the model with 20000 iterations or…

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Allen Institute for AI (AI2) hiring Head of Bioinformatics at Stealth Life Science Startup in Seattle, WA

About UsWe are an early stage startup using generative AI to fundamentally change life sciences research and accelerate the pace of biomedical discovery. Genomic data are at the heart of most modern molecular studies and tools, from basic research to clinical decision support, but these data are hard to work…

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What Type Of Software Application Is RStudio

Features of RStudio RStudio is a powerful integrated development environment (IDE) specifically designed for the R programming language. It offers a wide range of features that enhance the efficiency and productivity of R programmers. Let’s explore some of the key features of RStudio: Intuitive Code Editing: RStudio provides a clean…

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Need help improving image quality of a plot in ggplot – General

I have created this plot using ggplot in R and am struggling to get a polished finish:I exported the file as a JPEG and PNG and it always seems a little pixelated, especially the black circle, is there an easy way to fix this? I would also like to add…

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ggplot does not display a diagram – rstudio

Essentially, creating a dataframe and even the ggplot data seems to work, my laptop just does not want to display the data graphically. According to this video: you should be able to see the data when clicking on “plots”, however in my case just nothing happens as shown in my…

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Course – Introduction to R Shiny

Dear all, Unlock the potential of R Shiny and elevate your data visualization skills! Join our upcoming workshop, “Introduction to R Shiny” held online on January 29-30, 2024. Overview: Explore Shiny, an R package that transcends its classification, emerging as a powerful framework for crafting sophisticated web applications. Delve into…

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staRdom error – Fluorescence data processing – rstudio

I am trying to clean up my fluorescence data using staRdom package (script below), but I keep getting this error: Error in eem_raman_normalisation2(eem_list, blank = “Blank_correction”) : ****** First argument must be of class eemlist, second argument must be ‘blank’ for a blank correction, a number for correction with this…

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Line chart with multiple columns – ggplot2

library(dplyr) #> #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #> #> filter, lag #> The following objects are masked from ‘package:base’: #> #> intersect, setdiff, setequal, union library(ggplot2) library(stringr) library(tidyr) # original values of “0” and “1” converted to logical d <- structure(list(AN_BASE = c(2003,…

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Predicting missing values splines DESeq2

Hello, I am fitting splines in DESeq2 like so: dds <- DESeqDataSetFromMatrix(countData = counts, colData = coldata, design = ~ ns(age_scaled, df = 3)) Plotting later using the code Mike Love posted elsewhere: dat <- plotCounts(dds, gene, intgroup = c(“age”, “sex”, “genotype”), returnData = TRUE) %>% mutate(logmu = design_mat %*%…

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Python vs. R Studio: Choosing Your Path in Data Science and Analytics | by Codingmadeeasy | Nov, 2023

In the realm of data science and analytics, two prominent programming languages, Python and R, have garnered significant attention and loyal communities. Python, known for its versatility, and R, celebrated for its statistical capabilities, offer distinct advantages and cater to different needs within the field. Understanding their differences can aid…

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DESeq2 design with unbalance data and a multifactor design

Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…

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Bioconductor – ggsc

DOI: 10.18129/B9.bioc.ggsc   Visualizing Single Cell Data Bioconductor version: Release (3.18) Useful functions to visualize single cell and spatial data. It supports both ‘SingleCellExperiment’ and ‘Seurat’ objects. It also supports visualizing the data using grammar of graphics implemented in ‘ggplot2’. Author: Guangchuang Yu [aut, cre, cph] , Shuangbin Xu [aut]…

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DESeq2 with unbalanced dataset and multifactor design

Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…

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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…

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Solved I keep getting this error when trying to load my data

Transcribed image text: Chunk 1 : R. Markdown : Console Terminal x Background Jobs × R.3.1 ∼1 > library (ggplot2) > library (dplyr) > setwd (“c:/Users/Natiaye/Down Toads”) > mtcars <- read.csv (“mtcars”) Warning: cannot open file ‘mtcars’: No such file or directoryerror in file(file, “rt”) : cannot open the connection…

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Function Repository Quiz 1 NO GGPLOT .pdf – Function Repository 14 September 2022 01:08 PM Data Reading read csv /filename skip = value Reads

Data Reading read_csv(“/filename”, skip = value)Reads default csv’s and skips the value number of rows. Library(readr) read_tsv(“/filename”, skip = value)Reads default tab seperated sheets and skips value number of rows. Library(readr) read_delim(“/filename”,delim = “delimiter”, col_names = FALSE)General reading function, specifying the delimiter, saying we have no column names to assign…

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Bioconductor – dreamlet

DOI: 10.18129/B9.bioc.dreamlet   Cohort-scale differential expression analysis of single cell data using linear (mixed) models Bioconductor version: Release (3.18) Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of…

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r – Create a new custom point shape for ggplot2

I would like to use a new point shape on ggplot2, and use it the same way as geom_point(). I know that ggstar implements some new shapes, but I would like to use the following: It’s created just combining a circle with a rect, creating this new shape I think…

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Bioconductor – TxDb.Hsapiens.UCSC.hg38.knownGene

DOI: 10.18129/B9.bioc.TxDb.Hsapiens.UCSC.hg38.knownGene     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see TxDb.Hsapiens.UCSC.hg38.knownGene. Annotation package for TxDb object(s) Bioconductor version: 3.9 Exposes an annotation databases generated from UCSC by exposing these as TxDb objects Author: Bioconductor Core Team, Bioconductor Package Maintainer <maintainer at…

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Bioconductor – scDesign3

DOI: 10.18129/B9.bioc.scDesign3   A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics Bioconductor version: Release (3.18) We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning…

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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…

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Bioconductor – TCGAbiolinks

DOI: 10.18129/B9.bioc.TCGAbiolinks     TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data Bioconductor version: Release (3.5) The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses…

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r – Custom x-axis labels not applying correct custom x-axis colours

Using external vectors (a here) in non-NSE elements of ggplot2 expressions can be problematic, since the order of how a is applied is not necessarily (often is not at all) the same as the order of the columns. I suggest putting the colors into the frame itself. I’m inferring that…

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Bioconductor – iCOBRA

DOI: 10.18129/B9.bioc.iCOBRA     Comparison and Visualization of Ranking and Assignment Methods Bioconductor version: Release (3.6) This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a shiny application for interactive exploration of results. Author: Charlotte Soneson…

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Bioconductor – receptLoss

DOI: 10.18129/B9.bioc.receptLoss   Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors Bioconductor version: Release (3.18) receptLoss identifies genes whose expression is lost in subsets of tumors relative to normal tissue. It is particularly well-suited in cases where the number of normal tissue samples is small, as the…

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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…

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duplicates issues when trying to convert long to wide in R

duplicates issues when trying to convert long to wide in R 1 library(dplyr) library(tibble) library(tidyr) df <- test %>% mutate(row_id = model_name) %>% pivot_wider(names_from = gene_symbol, values_from = fpkm) ### Warning message: Values from `fpkm` are not uniquely identified; output will contain list-cols. • Use `values_fn = list` to suppress…

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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….

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Installing “separate” package (Newbie difficulty) – rstudio

Newbie here… I am 7/8ths of the way through the Data Analysis with RStudio course in Coursera… I’ve been doing quite well but have suddenly been stymied with a seemingly very simple operation. image_2023-11-09_105059608674×712 190 KB I have been tasked with splitting the names in the “name” column into two…

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r – Scatter graph coming out wrong

I am currently trying to create my scatter graph containing two different data’s, however I do not know what I am doing wrong as the graph is coming out completely wrong. This is what I coded: library(dplyr) library(ggplot2) library(tidyverse) conflict_rate <- read_csv(“https://raw.githubusercontent.com/owid/owid-datasets/master/datasets/Conflict%20deaths%20by%20country%20%E2%80%93%20UCDP%20(2019)/Conflict%20deaths%20by%20country%20%E2%80%93%20UCDP%20(2019).csv”) colnames(conflict_rate)[colnames(conflict_rate) == “Violent deaths in conflicts and one-sided…

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Import a Bioconductor package that is only used in a vignette/.Rmd script

My Bioconductor package is receiving Errors about a package not existing. I have an R package with Bioconductor. In the vignettes folder, I have several .Rmd files that have the following chunk at the top: title: ‘Manuscripts’ package: pkgName bibliography: pkgName.bib output: **BiocStyle**::html_document: toc_float: true tidy: TRUE border-width: 5px vignette:…

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Solved Please let me know how to do this using RStudio.When

Please let me know how to do this using RStudio. When conducting the simulation, fix the seed number as 20231027. The starwars dataset, which represents characteristics of characters from the Star Wars movies, is built into the dplyr package. Here’s the problem translated into English: A. Load the package required…

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Microarray data analysis with and without contrast

I have 6 samples of control and test condition normalized microarray intensities which Im using a starting point of my analysis. This is my basic analysis code library(readxl) library(dplyr) library(tidyverse) library(limma) # t # Create a data frame with the sample names and group names metdata <- data.frame( SampleName =…

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ggplot2 – Plotting convex hulls in R using ggplot/ggmap

Closed. This question needs to be more focused. It is not currently accepting answers. Want to improve this question? Update the question so it focuses on one problem only by editing this post. This post was edited and submitted for review 1 hour ago. I’m interested in plotting a polygon/convex…

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r – How to programmatically implement flexibility to either apply a column or use a single color to fill argument in ggplot

I am creating a custom function that generates bar plots using ggplot2 and geom_col(). My objective is to enable the function to dynamically assign either a single color or a color based on a grouping variable to the fill aesthetic. Here’s the code I’ve developed: library(ggplot2) library(dplyr) library(RColorBrewer) f1 <-…

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Looking at Eigenvectors as a Represention of a Process in R/RStudio using Mtcars | by Josef Waples

The typical calculation of an eigenvector involves solving the following equation: Av = λv where A is the square matrix, v is the eigenvector, and λ is the eigenvalue. By multiplying both sides of this equation by the matrix A and subtracting λv from both sides, we get: A(Av) -…

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Using easyPubMed and scholar package to get all citations of your paper

This is a tutorial on downloading all the citations for the articles present in any Google Scholar Profile. Use Case You might want to do it for your CV or help a friend. Update your lab website with the latest publication list. You might want to add all your published…

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loops – Force do not occur R Session Aborted in RStudio

I’d like to create a loop for several GLMM models, but I know that some factor is not possible to fit. I create some parameters to avoid errors like skip_to_next <- FALSE, tryCatch, and a minimum of points restriction (if(length(unique(NEW_DS_F_pred_sub$DATE))>=4)). Despite all of these steps I always have R Session…

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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…

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