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Tag: .csv
raster – Downloading ERA5 Reanyalysis Single Level wind data from copernicus using RStudio
I want to 1.) download and process wind data from the Era5 single layer cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels?tab=overview dataset using RStudio. The goal is to have a timeseries of several years of dailymean_windspeed (and direction) of an area (e.g. (57, 2, 51, 8). Calculating the daily means of u- and v- windcomponents prior…
Phenotypic profiling of solute carriers characterizes serine transport in cancer
Cell culture All cell lines used in this study were cultured at 37 °C in 5% CO2 in a humidified incubator. Human cell lines were authenticated by STR profiling using Promega GenePrint 10 and tested for Mycoplasma using Mycoalert (Lonza). Other than HCT116 p21−/− (a gift of B. Vogelstein60) all cell…
Re-create MNIST Dataset in Pytorch
I am newbie in Pytorch and in spite of quite a search, I am unable to grasp some concepts on datasets. Say I retrieve the MNIST dataset as follows import torch import torchvision data = torch.utils.data.DataLoader( torchvision.datasets.MNIST(“/Users/Myself/PyTorch_tutorials”, transform=torchvision.transforms.ToTensor(), download=True), batch_size=128, shuffle=True) took me a while to understand a DataLoader object…
How can I get not only variables’ names from R into Excel, but also the comments of the variables’ names? – General
Hi all, I’m an R-beginner… I have received a .sav-file, which I have imported into RStudio. Since I want to look at the data in Excel as well, I have converted it into an .csv-file using the write.csv function. My problem is now that in RStudio the names of the…
Fastest way to convert BED to GTF/GFF with gene_ids?
This is probably a duplicated question from: How To Convert Bed Format To Gtf? How to convert original BED file to a GTF ? Converting different annotation file formats (GTF/GFF/BED) to each other How to change scaffold.fasta file or scaffold.bed file to GTF file? Convert bed12 to GFF convert bed12…
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,…
Lab0 Manual – Lab 0: Introduction to RStudio Overview The goal of this lab is to introduce you to R
Lab 0: Introduction to RStudio Overview The goal of this lab is to introduce you to R and RStudio, which you will be using throughout the course both to learn the statistical concepts discussed in the class and also to analyze actual data and come to informed conclusions. R is…
Solanum lycopersicum and BC204 RNAseq data
Plant biostimulants have been earmarked as one of the major groups of new plant growth promoting substances to drive a much-needed revolution in agriculture. One such PB, BC204, has been used to great success, but there is no peer-reviewed data to explain the possible mechanisms by which it exerts its…
How can I adjust Y-axis scale when making relative abundance box plot ?
I am creating a relative abundance boxplot comparing two groups (pet, stray) using eight genera. However, the resulting plot displays not pretty in box shape. The reason is too wide variance of the Y-axis data. I assume that 1) eliminate Y-axis outlier and 2) Use log transformation with the relative…
Longitudinal detection of circulating tumor DNA
Analysis of Roche KAPA Target Enrichment kit experimental data obtained on an Illumina sequencing system is most frequently performed using a variety of publicly available, open-source analysis tools. The typical variant calling analysis workflow consists of sequencing read quality assessment, read filtering, mapping against the reference genome, duplicate removal, coverage…
Making multiple box plots with relative abundance in R
I am creating a relative abundance boxplot comparing two groups (pet, stray) using eight genera. However, the resulting plot displays almost zero values on the y-axis and only one value on the x-axis. I aim to generate a boxplot comparing the relative abundance of eight genera across two groups (pet,…
Dryad | Data — Native herbivore browsing alters plant physical and chemical traits in a eucalypt forest understory
README: Native herbivore browsing alters plant physical and chemical traits in a eucalypt forest understory Dataset contains six excel files containing raw data used for calculations of trait values for nine species in an open eucalypt understorey under two herbivory treatments. Data is also used to calculate community weighted means…
Python || Download dataset from kaggle and upload to Amazon S3 bucket without local storage in between
below script downloads a dataset from Kaggle, saves it on my local computer and uploads it to Amazon S3. Since I would like to host my script online and schedule a daily run I need to avoid storing the dataset on my local computer. What is the best way to…
Solved PICK A .csv dataset FROM KAGGLE and use python.
PICK A .csv dataset FROM KAGGLE and use python. Ensure all your code is well–commented. Each section should be clearly demarcated with Comments. All plots should have relevant titles, x and y–axis labels, and legends where necessary. Your comments on visual and numerical results should be based on the evidence…
Solved Use phyloseq for the question. Here is the
Use phyloseq for the question. Here is the dataset: [1] “BW1_sub_R1_trimmed.fq” “BW1_sub_R2_trimmed.fq” [3] “BW2_sub_R1_trimmed.fq” “BW2_sub_R2_trimmed.fq” [5] “filtered” “R10_sub_R1_trimmed.fq” [7] “R10_sub_R2_trimmed.fq” “R11_sub_R1_trimmed.fq” [9] “R11_sub_R2_trimmed.fq” “R11BF_sub_R1_trimmed.fq” [11] “R11BF_sub_R2_trimmed.fq” “R12_sub_R1_trimmed.fq” [13] “R12_sub_R2_trimmed.fq” “R1A_sub_R1_trimmed.fq” [15] “R1A_sub_R2_trimmed.fq” “R1B_sub_R1_trimmed.fq” [17] “R1B_sub_R2_trimmed.fq” “R2_sub_R1_trimmed.fq” [19] “R2_sub_R2_trimmed.fq” “R3_sub_R1_trimmed.fq” [21] “R3_sub_R2_trimmed.fq” “R4_sub_R1_trimmed.fq” [23] “R4_sub_R2_trimmed.fq” “R5_sub_R1_trimmed.fq” [25] “R5_sub_R2_trimmed.fq” “R6_sub_R1_trimmed.fq” [27] “R6_sub_R2_trimmed.fq”…
Solved Use phyloseq for this question. Here is the dataset:
Use phyloseq for this question. Here is the dataset: [1] “BW1_sub_R1_trimmed.fq” “BW1_sub_R2_trimmed.fq” [3] “BW2_sub_R1_trimmed.fq” “BW2_sub_R2_trimmed.fq” [5] “filtered” “R10_sub_R1_trimmed.fq” [7] “R10_sub_R2_trimmed.fq” “R11_sub_R1_trimmed.fq” [9] “R11_sub_R2_trimmed.fq” “R11BF_sub_R1_trimmed.fq” [11] “R11BF_sub_R2_trimmed.fq” “R12_sub_R1_trimmed.fq” [13] “R12_sub_R2_trimmed.fq” “R1A_sub_R1_trimmed.fq” [15] “R1A_sub_R2_trimmed.fq” “R1B_sub_R1_trimmed.fq” [17] “R1B_sub_R2_trimmed.fq” “R2_sub_R1_trimmed.fq” [19] “R2_sub_R2_trimmed.fq” “R3_sub_R1_trimmed.fq” [21] “R3_sub_R2_trimmed.fq” “R4_sub_R1_trimmed.fq” [23] “R4_sub_R2_trimmed.fq” “R5_sub_R1_trimmed.fq” [25] “R5_sub_R2_trimmed.fq” “R6_sub_R1_trimmed.fq” [27] “R6_sub_R2_trimmed.fq”…
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…
How to use awk and grep -v option to exclude several patterns from several lines
How to use awk and grep -v option to exclude several patterns from several lines 1 I am trying to use a combination of awk and grep to filter several files and to exclude a couple of patterns. I have several options and I just get error. My commands that…
How to Install DataSpell on Linux: A Comprehensive Guide
With the boom of AI and data science, there’s a rise in the need for data scientists and machine learning engineers as well. Those engineers and developers need tools like an IDE to write their code and train models. A specialized IDE can enhance their workflow and improve their efficiency….
A Bioconductor workflow for processing, evaluating,…
Introduction Proteins are responsible for carrying out a multitude of biological tasks, implementing cellular functionality and determining phenotype. Mass spectrometry (MS)-based expression proteomics allows protein abundance to be quantified and compared between samples. In turn, differential protein abundance can be used to explore how biological systems respond to a perturbation….
Whole Plasmid Sequencing Details
Sample Preparation Sample type Size Category Length Concentration Min volume Price per sample Plasmid Regular 2.5 – 25 kb 30 ng/uL ≥10 uL $15 Large 25 – 125 kb 50 ng/uL ≥20 uL $30 XL 125 – 300 kb 50 ng/uL ≥40 uL $60 Linear/Amplicon Standard 600 bp – 25…
student gets one Excel quiz or one RStudio quiz. 20
Transcribed image text: student gets one Excel quiz or one RStudio quiz. 20 scores from each from each course are randomly selected and observed. The data is given in the file below. Download .csv file A. The differences in the grades using Excel and the grades using RStudio are normally…
and one RStudio quiz the order of which is first is
Transcribed image text: and one RStudio quiz the order of which is first is random. 20 business school students scores are observed. The data is given in the file below. Download .csv file Rank Test]. What statement below aligns with your findings? A. Heteroscedasticity among the groups B. The differences…
how to assign chromosome-level annotation to a genome organised by contig?
0 I am working with genomic data and I am trying to do GWAS analysis with a dataset where I compare two populations of a bird species. I have a good reference genome (ordered by contig size) and resequence data from several individuals of 2 different populations. I did 1)…
Looking to Boost Your Store’s Performance? Let’s Crack the Code of Shopper Habits | by Yilin Wu | Oct, 2023
Unveiling Market Basket Analysis with Apriori in Python to Reveal Customer Insights Photo by Boxed Water Is Better on Unsplash Market basket analysis spills the beans on customer buying habits. It’s like peeking into a shopper’s cart and discovering a world of item combinations tailored to individual tastes. This clever…
NIST MS Search and results
NIST MS Search and results 0 Hey guys, what’s up? Follow, I’m using the NIST MS Search to compare Unknown Spectras with Spectras from MoNA (MassBank of North America) and he shows a great software for this. But, my problem is: how to export ALL the results for a .csv…
Use ABH formated Genetic map to scaffold contig level genome assembly to Scafold level assembly.
Use ABH formated Genetic map to scaffold contig level genome assembly to Scafold level assembly. 0 I have a Genetic map (18000_markers.csv) in ABH format and i want to use this genetic map to scaffold a contig level assembly(I have 2 haplotype phased genome assembly). I figured out that this…
dataframe – Is there an easy way in R to use a separate “Values” vector (of unique keys) to map as a ggplot axis for a visualization?
New to the R universe and having trouble conceptualizing this problem I seem to be having with ggplot + R. With the data set I have, I’m trying to map individuals (by their Id keys) over their activity (dates). With the data frame I have which I’ve labelled “fitbitdaily”. When…
python – Creating pytorch dataset from one .csv file
I have a .csv file where I keep all the info my model needs to use, and I’m trying to do Cross Validation in PyTorch for my model. My original Idea was to use sklearn.model_selection.cross_validate or similar functions, as I’m using the scoring functions from sklearn to score my model…
Solved In Lesson 3 you learned some helpful shortcut keys.
Transcribed image text: In Lesson 3 you learned some helpful shortcut keys. To create a new script file in RStudio you can use the shortcut keys: Ctrl + Shift + To set your working directory in RStudio you can use the shortcut keys: Ctrl + Shift + Question 2 3…
I need help with RStudio and how to accomplish
I need help with RStudio and how to accomplish the exercise: 1) Download and upload the insurance data into RStudio (it is a .csv file) a. Here is what the columns in the dataset are: claimid incident_date claim_type uninhabit claim_amount fraudulent policy_id policy_date coverage deductible townsize gender dob ed_cat job_start…
r – Slurm job array pulling parameter set from .txt file and using parameters as objects in Rscript
I am currently trying to run a stochastic simulation in R using changing parameters by submitting a slurm array job to HPC. I have stored the parameters in a .txt file where each line contains the parameter iteration to be set as individual objects in R before running simulation (e.g….
python – Can I modify entries in a Pytorch Dataset object?
I’ve taken code from the Pytorch Geometric website, namely: link to Pytorch Example Notebook It uses the MUTAG dataset, which has 188 graphs. I’ve tried to modify the first 59 graphs to become specific graphs with features and labels that I’ve created. So effectively I wanted to overwrite the first…
During your second Individual Project (IP), you will
During your second Individual Project (IP), you will utilize your Python environment to derive structure from unstructured data. You will utilize the data set “Airline Sentiment” from Kaggle open data sets located at www.kaggle.com/welkin10/airline-sentiment. Using this data set, you will create a text analytics Python application that extracts themes from…
Bioconductor Config
Showing : Config • reset 1 result • Page 1 of 1 Recent … Replies Answer: DEG data by James W. MacDonald 63k This support site is intended to help people who have specific questions about Bioconductor packages, rather than as an advice site meant t… Answer: diffbind by Rory…
From Kegg – Kaas to MetaCyc
From Kegg – Kaas to MetaCyc 2 Hello all, I need help using Metacyc. I just finished running my experiment in KEGG – Kaas, analyzing metabolic pathways for the illumina transcriptome (RNA) sequencing data we have, mapping them to Eukaryotes. I may like to run the same experiment in Metacyc…
Hands-On Natural Language Processing with PyTorch 1.x: Build smart, AI-driven linguistic applications using deep learning and NLP techniques 9781789802740, 1789802741
File loading please wait… Citation preview Hands-On Natural Language Processing with PyTorch 1.x Build smart, AI-driven linguistic applications using deep learning and NLP techniques Thomas Dop BIRMINGHAM—MUMBAI Hands-On Natural Language Processing with PyTorch 1.x Copyright © 2020 Packt Publishing All rights reserved. No part of this book may be reproduced,…
import file (.csv) too big to import to vertex ai …
I have image dataset of receipts of about 12gb along with their label and bounding boxes (.json) of about 800 mb. I have uploaded the images dataset successfully to gcp bucket and created the cloud storage path in CSV. I then combined the path with the label and bounding boxes…
r – Trouble making a particular sampling schematic diagram using ggplot2 and ggforce
I’ve been trying to make a reproducible version of a diagram of the sampling scheme for a particular field project, mirroring this version that I made by hand in PowerPoint: Original sampling schematic figure Geom_mark_rect from ggforce has been super helpful for creating boxes around the collections of points. However,…
google cloud platform – unable to use the dataset in format .xlsb in Vertex AI for Time Series Forecasting
I am trying to import the data in Vertex AI . The Dataset is in .xlsb Format it requires me to convert them into .csv Files but during conversion it erases a a lot of data. Also when I try to seperately load the data ,In The BigQuery it cannot…
Logistic Regression in RStudio: Revealing Secret Discoveries!
Unveiling the Power of Logistic Regression in RStudio for Predictive Analysis Key Points Unlock hidden insights with Logistic Regression in RStudio: A beginner’s guide to predictive analytics. Master Logistic Regression in RStudio with step-by-step instructions and practical examples. Discover real-world applications of Logistic Regression: from medical research to fraud detection….
Fastq manifest import error – Technical Support
hdeel (Heather Deel) July 7, 2023, 4:55pm 1 Hello Q2 folks, Hope you all are well. I am having issues importing some demultiplexed 18S data into qiime2-2023.5, and after a good while searching on the forum and troubleshooting, I keep getting the same error. Here is the command:qiime tools import…
Outformat support for EMBL-EBI RADAR (Rapid Automatic Detection and Alignment of Repeats in protein sequences)
Outformat support for EMBL-EBI RADAR (Rapid Automatic Detection and Alignment of Repeats in protein sequences) 0 I’ve been using RADAR on EMBL’s web service through the command line with the rest API. The documentation (below) suggests I should be able to output the results as a CSV but I have…
Creating a Histogram in R: A Step-by-Step Guide
Hi there! Are you interested in how to make a histogram in R? Well, you’re in luck because in this article, we’ll provide a simple introduction to creating histograms in R. A histogram is a graphical representation of a frequency distribution of numerical data, where the data are divided into…
OSError: [Errno 30] Read-only file system [Solved]
# OSError: [Errno 30] Read-only file system [Solved] The “OSError: [Errno 30] Read-only file system” occurs when you pass a non-existent path to an os method or try to write to a read-only directory. To solve the error, make sure that the path you’ve passed to the method is correct…
Dryad | Data — Supplementary material for: Accounting for within-species variation in continuous trait evolution on a phylogenetic network
This supplementary material contains data and scripts for (1) a simulation study assessing the performance of our phylogenetic comparative method on trait data generated using an actual species network, and (2) a comparative analysis of how Polemonium leaflet size covaries with geographical predictors, assuming either a reticulate or non-reticulate time-calibrated…
how to export data from rstudio to excel
You need to write the path of the file in the function drop_delete(), We can summarize all the functions in the table below, Copyright – Guru99 2023 Privacy Policy|Affiliate Disclaimer|ToS, How to Export a DataFrame to a CSV File in R, How to Export a Data from R to Excel…
Solved Use Rstudio. This is the information from labdata3
Use Rstudio. This is the information from labdata3 shown in R. ID,major,job_offers,age,extra,leader,role,intern,research,prm_2yr,years,salary,rating1,IST,1,22,2,10,Treasurer,1,24,No,5,91799,Meets Expectations2,IST,7,26,3,15,Secretary,4,25,Yes,6,103922,Exceeds Expectations3,IST,8,21,1,6,Member at Large,1,6,No,4,86984,Meets Expectations4,IST,5,26,0,0,Member at Large,1,0,No,2,63095,Below Expectations5,IST,4,22,1,6,Secretary,2,42,Yes,3,73405,Meets Expectations6,IST,4,23,1,6,Secretary,2,12,No,3,74926,Below Expectations7,IST,4,30,1,6,Treasurer,3,35,Yes,4,82661,Meets Expectations8,IST,9,23,2,12,Treasurer,4,38,Yes,5,95945,Exceeds Expectations9,IST,15,21,5,25,Vice President,1,16,No,7,117350,Meets Expectations10,SRA,7,29,2,12,Member at Large,2,16,No,4,89808,Meets Expectations11,SRA,12,27,5,30,Vice President,2,19,Yes,7,115837,Meets Expectations12,SRA,8,23,1,6,Vice President,4,3,Yes,4,85864,Meets Expectations13,SRA,3,26,1,6,Member at Large,2,12,Yes,4,84844,Meets Expectations14,SRA,12,28,4,24,Vice President,4,45,Yes,7,111411,Meets Expectations15,SRA,1,21,5,30,Vice President,2,47,No,7,116061,Meets Expectations16,SRA,7,26,3,18,Treasurer,2,22,Yes,6,101367,Meets Expectations17,SRA,16,26,0,0,Member at Large,4,17,Yes,5,65493,Meets Expectations18,SRA,2,24,4,24,Secretary,3,34,Yes,6,104613,Exceeds Expectations19,Cyber,1,27,1,6,Member at Large,1,34,No,4,84821,Meets Expectations20,Cyber,3,29,1,6,Vice President,3,5,No,3,77076,Below Expectations21,Cyber,7,25,3,18,Secretary,1,26,No,6,103505,Meets…
Traits and roadkill rates data for Brazilian reptile species
Data for the paper “ASSESSING BRAZILIAN REPTILES’ ROAD-KILL RISKS USING TRAIT-BASED MODELS”. This collection includes: [1] one *.rmd file that contains the R code used for analysis (“script_RandomForest_BrazilianReptileRoadkills.Rmd”); [2] six *.csv files with roadkill data for Brazilian reptiles (“roadkill_data.csv”, “roadkill_data2.csv”, “roadkill_data3.csv”, “roadkill_data4.csv”, “roadkill_data5.csv” and “roadkill_data6.csv”); [2.1] “roadkill_data.csv” is the data…
python – GCP: gcoud ai-platform jobs list –project my-project-id fails to list projects, when Vertex AI UI shows models are training
Google Vertex AI job appears to be running in UI, after starting job from UI, but “gcloud ai-platform jobs list –project my-project-id” command shows “Listed 0 items.” Steps I followed: Upload my dataset from .csv file. I select the “train new model” button in datasets UI. I select “other” I…
Converting Microarray SNP data into VCF format
Converting Microarray SNP data into VCF format 1 Hello everyone, I have only one microarray data which contains one .CEL file and another intensity .csv file. I’m searching for converting any of the two files into vcf format. After going through Biostars and Bioconductor forums, I found pd.genomewidesnp.6@getdb, crlmm and…
Bioinformatics/Python: a quick help needed with a simple data analysis
Job Description: Hi there, For those of you familiar with bioinformatics, I have an input .csv file (attached) that contains a table with Uniprot IDs that correspond to the proteins of my interest. For each organism listed in the column A, I need to calculate the average % of I,…
Using multiple gpus (ddp pytorch) and showing loss graphs by dis.reduce – vision
SM2023 (SUN) May 11, 2023, 4:31am 1 Hi All, I am using ddp pytorch for fine tunning my model. I am wondering how I can save the average of loss function from all gpus for showing the loss graph. when I printing the loss in the code, it shows me…
Illumina TruSeq Stranded total Sample Preparation Protocol | CHMI services – TruSeq Stranded Total RNA
Preparation of total transcriptome libraries for sequencing on an Illumina dais Edit me Documentation TruSeq Running Absolute RNA Sample Prep Guide. This method makes a cDNA library of all RNA molecules presentational in your spot after rRNA depletion. Important: the succeed of this kit is dependent on of ability of…
PinAPL.py – – Antibody Capture and CRISPR Guide Capture Analysis -Software …
Enter a project name for your analyze runner. This name will help you identify insert final in case yours do manifold runs in a brawl. Provision of an email site exists optional, but desires rented you safely close the browser during the analysis and receive a notification following verwirklichung. Upload…
can you slove part 1 and part 2 from this this lab
Transcribed image text: Lab Description In this lab, we will learn about decision tree classifiers and walk through an example of how to create decision trees using Scikit-Learm. We’ll see how the algorithm works with both numeric and non-numeric data. We will also leam how to evaluate the algorithm’s accuracy…
deep learning – PyTorch model not converging in a CNN + LSTM classification task
I am training a PyTorch model to classify spectrograms of audio signals into two classes (normal, abnormal) using a CNN followed by an LSTM. The CNN is used to extract time features, and the LSTM is used to classify the spectrograms. The input shape to the LSTM is [batch_size, 64,…
Gnu Parallel – Parallelize Serial Command Line Programs Without Changing Them
Article describing tool (for citations): O. Tange (2011): GNU Parallel – The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47. Author’s website for obtaining code: www.gnu.org/software/parallel/ All new computers have multiple cores. Many bioinformatics tools are serial in nature and will therefore not use the multiple cores. However, many…
Pytorch torchvision.datasets.ImageFolder FileNotFoundError: Found no valid file for the classes – vision
These folders does not contain anything. For Wiki Crop data I have convert .mat file to csv.‘’’import numpy as npfrom scipy.io import loadmatimport pandas as pdimport datetime as datefrom dateutil.relativedelta import relativedelta cols = [‘age’, ‘gender’, ‘path’] wiki_mat = ‘/content/drive/MyDrive/wiki_crop/wiki.mat’ wiki_data = loadmat(wiki_mat) del wiki_mat wiki = wiki_data[‘wiki’] wiki_photo_taken =…
Merging more than 2 csv files in R
Merging more than 2 csv files in R 2 Hello! How do I merge more than two csv files in R based on gene_id and log2.fold_change? Is there a easy code or package for it? Thank you. merge r • 4.3k views • link updated 2 hours ago by zx8754…
r – File not found with knitr::include_graphics in rmarkdown via RStudio when data and pdf-image present
I use win10 system and have the following file tree C:\Users\xxx\Desktop\islr C:\Users\xxx\Desktop\islr\data\Advertising.csv C:\Users\xxx\Desktop\islr\fig\2-1.pdf I have some .csv data sets and .pdf figures from www.statlearning.com/resources-first-edition; or you can test my demo.rmd using any .csv data and .pdf figure available at hand. My demo.rmd reads as follows: — title: “TTT” author: “aaa”…
Dryad | Data — RNAseq transcriptome of draining lymph node (LN) and tumor of MC38 murine tumors treated with cryoablation and chitosan/IL-12
Focal ablation technologies are routinely used in the clinical management of inoperable solid tumors but often result in incomplete ablations leading to high recurrence rates. Adjuvant therapies capable of safely eliminating residual tumor cells are therefore of great clinical interest. Interleukin 12 (IL-12) is a potent antitumor cytokine that can…
rstudio – Copy a selected column in shiny into a new dataframe to work with
Ih have CSV Files who are not the same. Each Study I have to do has other quantity and names of columns. So I have write an shiny app and have no problem to import the first table (data). But for capability analysis I will choose the column in dropdown…
How to import dataset from other software into DESeq2?
How to import dataset from other software into DESeq2? 0 @ddf74715 Last seen 12 hours ago United States Hi, I am new to the DESeq2, and I wonder if the dataset (either .csv or .txt) prepared from other program can be imported to DESeq2 as a form of DESeqDataSet in…
Solved In this problem the goal is to build a set of
Transcribed image text: In this problem the goal is to build a set of numerical images from a set of arrays. The data set is from the Kaggle web site will be used: www.kaggle.com/c/digit-recognizer/data This data has a training.csv, test.csv and sample submission.csv files. In this exercise the focus will…
UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0x8b in position 1: invalid start byte
I use python package to load and analysis vcf.gz files, for ch in chs: vcf_to_1240K_hdf(in_vcf_path = f”/mnt/gpfs/Users/wangjincheng/aDNA/All_data/Analysis4/19.genotype_imputation/GLIMPSE_test/GLIMPSE_ligated/merged_chr{ch}.vcf.gz”, path_vcf = f”/mnt/gpfs/Users/wangjincheng/aDNA/All_data/Analysis4/19.genotype_imputation/GLIMPSE_test/ancIBD/chr{ch}.vcf”, path_h5 = f”/mnt/gpfs/Users/wangjincheng/aDNA/All_data/Analysis4/19.genotype_imputation/GLIMPSE_test/ancIBD/chr{ch}.h5″, marker_path = f”/mnt/gpfs/Users/wangjincheng/aDNA/reference/data/filters/snps_bcftools_ch{ch}.csv”, map_path = f”/mnt/gpfs/Users/wangjincheng/aDNA/reference/data/afs/v51.1_1240k.snp”, af_path = f”/mnt/gpfs/Users/wangjincheng/aDNA/reference/data/afs/v51.1_1240k_AF_ch{ch}.tsv”, col_sample_af = “”, buffer_size=20000, chunk_width=8, chunk_length=20000, ch=ch) but get this error below: UnicodeDecodeError Traceback (most recent call last)…
DataSpell 2023.1 EAP 2 is Out!
Early Access Program News Many DataSpell users requested the ability to organize their work into multiple projects with completely separate environments and in DataSpell 2023.1 EAP 2 we have delivered! This second EAP build also contains new features to convert a Jupyter Notebook into a Python script and vice versa,…
[Solved] You must have .R or RStudio to do these problems. (I made a link to…
You must have .R or RStudio to do these problems. (I made a link to the .R files for each question) the link for .R’s website is here:cran.r-project.org/bin/windows/base/ Maybe you have them already, I tried to convert them into .csv files (for Excel or Minitab which I prefer)…
Nextflow output from different processes mixed up as input in later processes
I wrote a Nextflow workflow DSL2 with the output of some processes used in multiple processes later in the workflow. The last process is to print out a summary of the read counts after trimming and after the last step. I ran the pipeline for 2 pairs of fastq samples….
unable to import data into RStudio – General
I have been unable to import data file from the Coursera learning course that I am currently into. Here are the course note and instructions. Step 2: Import data One of the most common file types data analysts import into R is comma separated values files, or .csv files. The…
create txt file with path to execute gatk
create txt file with path to execute gatk 0 hello, I want to create paths to my vcf files inside a txt file. User/sample1/file.vcf User/sample2/file.vcf The problem is that I won’t use all the samples except those stored in a .csv file. Do you have a script to match and…
Interpreting ASCAT CNV output
Interpreting ASCAT CNV output 1 Hello, I have two queries w.r.t ASCAT CNV data: How does one go about getting the total copy number for a given locus or chromosome from the ASCAT CNV.output results. What is the optimal way to filter the dataset to reduce the noise? I would…
Fumarate induces vesicular release of mtDNA to drive innate immunity
Mice Mice were of mixed genetic background C57BL/6 and 129/SvJ. Mice were bred and maintained under specific-pathogen-free conditions at the Breeding Unit (BRU) at the CRUK Cambridge Institute. Fh1fl/fl (ref. 4) and R26-Cre-ERT2 (ref. 5) mice were gifts from E. Gottlieb and D. Winton, respectively. Experimental mice were homozygous for…
Difference-In-Difference Regression With 1 Moderator Variable. Causal Inference. – rstudio
I am creating a dataset in excel looking at the relationship between the monthly federal funds rate and monthly inflation (IV) and stock indices’ (DV) monthly % return. I performed the linear and multiple variable regressions on the data in Excel first. I was able to produce the R^2, Adjusted…
Bioinformatics Workshops: How to Find, Download and Process public RNA seq data to Analyze it with DESeq2 in RStudio *Online* – Yale Library Study Spaces Scheduling
Sequencing data is increasingly available in public repositories making it easier for reanalysis. Join us for this *online* session where we will explore the repository GEO RNA-seq Experiments Interactive Navigator (GREIN). We will focus on how to find bulk RNA seq datasets and which data tables should one download and…
Solved From Kaggle download TV, Newspaper and Radio
From Kaggle download TV, Newspaper and Radio advertisement budgets versus sales data. Thisdata set is also uploaded in python as .csv.1. What is the number of input feature (N)?2. A python code is given below to design parameters of the linear regression that minimizes theMSE and calculates the test error….
[8.15 MB] Download Free of Importing a .csv file to R Studio using the read.csv function Mp3 (05:56 Min)
Importing a .csv file to R Studio using the read.csv function (8.15 MB) – Free Download Importing a .csv file to R Studio using the read.csv function (05:56 Min) mp3 – Download lagu mp3 Importing a .csv file to R Studio using the read.csv function on MP3 Juice. Title Importing…
Solved Requirements For this assignment, complete the
Transcribed image text: Requirements For this assignment, complete the following requirements: 1. Research and locate a dataset stored as a .csv file from kaggle.com that interests you. Save the URL (web address) of the page you downloaded the dataset from that shows the information about the file. 2. The .csv…
Solved Use package ‘ggplot2’ to generate all the graplis in
Transcribed image text: Use package ‘ggplot2’ to generate all the graplis in HW4. 1. Stock Prices: – Check out the yahoo webpage of historical stock price data for Netflix (NFLX): finance. yahoo.com/quote/NFL X/history? p=NFLX ). – Change the range of Date from 01/01/2021 to 09/30/2021. Click on “Apply” before “Download”….
scikit learn – Create X train and Y Train for CSV dataset in Python
This seems a general question, but I can answer with: You can use following block to import these csv files in your env. import pandas as pd # for CSV file I/O operations train = pd.read_csv(‘../input/data_train.csv’) test = pd.read_csv(‘../input/data_test.csv’) I did not see your .csv files but it must be:…
github – Source control or Project folder connections with Jupyter
I need help in deciding the easiest approach to centralized the storage of all project-related files such as data extracts and python code which can then be accessed and executed into JypterHub without manually uploading into the JypterHub folder Can I store the updated version of the .ipynb file and…
Generating multiple heatmaps with heatmap3 and lapply
Generating multiple heatmaps with heatmap3 and lapply 1 Hey everybody I have a series of .csv files from RNA-seq data stored in a list and I am trying to produce a heatmap for each of them by using heatmap3 function combined with lapply in R, after first converting each of…
How to analyze Infinium Mouse Methylation BeadChip array data?
Hi! I played around with the Illumina mouse demo data and ENmix. The following code worked for me and you should end up with normalized beta values for subsequent limma analysis (or DMR analysis folowing the ENmix vignette). #setwd() #download the Infinium_Mouse_Methylation_v1.0_A1_GS_Manifest_File.csv file from Illumina HP to working directory (=…
Answer: Pathogen-drug network
Search google for “antibacterial **drug database**” you could change antibacterial with antimicrobial or other relevant terms. If you can find a database/tsv/csv file you could extract the information you need from it. I think this is the best one I found for antivirals: www.viprbrc.org/brc/antiviralDrug_search.spg?method=ShowCleanSearch&decorator=picorna_entero ———- This one might give you…
up-down regulated using log2FC
up-down regulated using log2FC 0 Hello, I used Data Wrangling in R to write commands to find the number of FC>1 and FC<1. But R recognizes the column “log2FC” as null. library(tidyverse) library(lubridate) library(stringr) targets <- read.csv(“FilteredGenes(STD-Met-Cin).csv”) glimpse(targets) targets <- tibble(‘log2FC ‘=targets$log2FC) glimpse(targets) unique(targets$ log2FC) summary (targets) targets<- tibble(‘log2FC’=targets$ log2FC)…
change name several files
My goal is to remove the second “column”, so the 10 in the first case, the 87 in the second and the 345 in the third. This statement is confusing. On one hand, you are (OP) saying you want to remove second column and on the other hand, you are…
How to export count data as .csv file in Seurat
How to export count data as .csv file in Seurat 1 Hi, I’m trying to export the log normalized count data from Seurat in to a .csv file and get the following error: library (Seurat) fib.data <- subset(onlyharmonfib, subset = nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mito <5)…