Tag: NA

CSIC Project Receives 1.9 Million Euros From The European Union To Develop More Sustainable And Safer Batteries

The work of researcher at the Institute of Materials Science of Barcelona (ICMAB-CSIC) Alexandre Ponroch has been recognized by the European Research Council (ERC) through a ‘Consolidator Grant’ 2022. Endowed with approximately 2 million Euros, this economic support will give researchers 5 years to develop the MultimetalBat project. The aim…

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python – Using Kaggle code/model to predict classifications for my dataset of sequences

I have obtained the following code along with a dataset from a Kaggle notebook: www.kaggle.com/code/danofer/predicting-protein-classification/notebook import pandas as pd import numpy as np from matplotlib import pyplot as plt import seaborn as sns from sklearn.feature_extraction.text import CountVectorizer from sklearn.model_selection import train_test_split from sklearn.metrics import accuracy_score, confusion_matrix, classification_report import sys #…

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admixture plot ggplot2

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct. ggplot2 is a well-known data visualization package to use in R. As ggplot2 is well developed from the beginning, engineers can spend more…

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r – Why is the ggplot not generating any plot?

I wanted to plot a animated plot using gganimate , here is the code: library(ggplot2) library(dplyr) library(reshape2) library(gganimate) rain<-read.csv(“csvrainfall.csv”) temp<- read.csv(“temp.csv”) mean_temp<-temp$Temp > #computing mean annual rain rain$mean_ann_rain<- apply(rain[,-1], 1, function(x) mean(x, na.rm=TRUE)) > #combining the two datasets combined_rain_temp<- cbind(rain, mean_temp) > #transforming the data from wide to long form…

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Fine-scale genomic tracking of Ross River virus using nanopore sequencing | Parasites & Vectors

Flaxman JP, Smith DW, Mackenzie JS, Fraser JRE, Bass SP, Hueston L, et al. A comparison of the diseases caused by Ross River virus and Barmah Forest virus. Med J Aust. 1998;169:159–63. Article  Google Scholar  El-Hage CM, Bamford NJ, Gilkerson JR, Lynch SE. Ross River virus infection of horses: appraisal…

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How to run a R for loop on data stored in data lake where there are multiple lines to a single row & column?

Sample illustration of the data in data lake looks like the following. I have tried the following code but the output is skipping the 0th line value for every column and row. Data_extract <- data[data$Row == ‘4’, ] Data_extract <- Data_extract[Data_extract$Line >= 0, ] line_count <- length(Data_extract[, “Row”]) line_num <-…

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Grid Dynamics Expands Relation – GuruFocus.com

Key Takeaways: Grid Dynamics will partner with Google to implement Google Cloud LLMs and Vertex AI solutions. The expanded Grid Dynamics relationship with Google Cloud reflects the company’s position as an industry leader in AI and enables the company to accelerate the development of innovative, industry-specific AI solutions for global…

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Grid Dynamics Expands Relationship with Google Cloud, Serving as

June 6, 2023 – 4:05 pm Key Takeaways: Grid Dynamics will partner with Google to implement Google Cloud LLMs and Vertex AI solutions. The expanded Grid Dynamics relationship with Google Cloud reflects the company’s position as an industry leader in AI and enables the company to accelerate the development of…

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Grid Dynamics Expands Relationship with Google Cloud, Serving as Global Partner for Implementing Innovative Generative AI Solutions

Key Takeaways: Grid Dynamics will partner with Google to implement Google Cloud LLMs and Vertex AI solutions. The expanded Grid Dynamics relationship with Google Cloud reflects the company’s position as an industry leader in AI and enables the company to accelerate the development of innovative, industry-specific AI solutions for global…

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2023-06-06 | NDAQ:GDYN | Press Release

Key Takeaways: Grid Dynamics will partner with Google to implement Google Cloud LLMs and Vertex AI solutions. The expanded Grid Dynamics relationship with Google Cloud reflects the company’s position as an industry leader in AI and enables the company to accelerate the development of innovative, industry-specific AI solutions for global…

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r – ggplot facet_wrap + multiple groups

This is my data I am working with: structure(list(Substrate = c(“Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Glukoza”, “Manoza”, “Manoza”, “Manoza”, “Manoza”, “Manoza”, “Manoza”, “Manoza”, “Manoza”,…

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Limma returned only positive logFC values

Limma returned only positive logFC values 0 I want to obtain the upregulated and downregulated genes using limma. However, all the DEGs returned by my code have positive LogFC and none are downregulated (negative LogFC). This observation is consistent across multiple distinct dataframes. Is there something wrong with my code?…

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r – Trim white space in ggplot modified raincloud plot with discrete variables

I’m having difficulty trimming white space from the discrete axis of a ggplot. See reprex below – how can I remove the white space between the data for “large” and the x-axis? I’ve tried various versions of scale_x_discrete but it doesn’t seem to have any effect. # Prepare data sample_data…

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Italicise annotations with pheatmap

Hello, I have some column annotations in a heatmap (generated with pheatmap), which correspond to species that i want to be in italics. I have read through the pheatmap documentation and I can’t find anything. I have also tried to find and adapt solutions online (for example), but most tutorials…

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How to have a hexagon shape tile grid map with ggplot2 in R

For the last week’s TidyTuesday challenge, I was trying to replicate a world tile grid map made in R, which can be accessible from here. Here is the code so far; library(tidyverse) library(ggplot2) library(tidytuesdayR) library(highcharter) library(maps) library(jsonlite) # Load the ‘jsonlite’ package library(showtext) library(showtextdb) library(ggtext) world_grid <- read_csv(“worldtilegrid.txt”) tt <-…

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r – Create groups based on contiguous rows for displaying in a ggplot line chart

I have an extended time series, and wish to highlight some trends of interest within the chart. Something along these lines: The problem is, the highlights could be high (red) or low (green), so I need to map a colour aesthetic to the chart as well. When I do so,…

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element_textbox function – RDocumentation

Usage element_textbox( family = NULL, face = NULL, size = NULL, colour = NULL, fill = NULL, box.colour = NULL, linetype = NULL, linewidth = NULL, hjust = NULL, vjust = NULL, halign = NULL, valign = NULL, lineheight = NULL, margin = NULL, padding = NULL, width = NULL,…

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Make a new column in R or bash

I have antibody data the first column is heavy chain sequence and the second column is the light chain I want to create a third column by combining two columns like If CARGRGIAVAGTTGFDYW is a heavy chain and CQQYNSYSLTF a light chain, in third column I want CARGRGIAVAGTTGFDYW_CQQYNSYSLTF if a…

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r – Missing one line in ggplot2 line graph and highlighting particular data in line graph

I’m working with some regional level data about household internet access in Latinamerica and the Caribbean, I made a df in order to use ggplot2 to do some graphic representations of my data and I encountered some problems. This is my commented code: library(ggplot2) library(tidyverse) library(scales) library(ggrepel) library(gghighlight) #Doing the…

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Table 1 | Primary Esophageal Lymphoma: A Histopathological Experience from Two Tertiary Hospitals, Western Saudi Arabia

Gastroenterology Research and Practice/ 2023/ Article/ Tab 1 / Research Article Table 1 Summary of the PEL cases diagnosed at KAUH and KFSH&RC, Jeddah. Age/sex Site Clinical presentation Diagnosis BM Tumor gross Follow-up (months) Treatment/outcome 1 68/M Lower esophagus Dysphagia and weight loss DLBCL −VE Polypoid mass 15 R-CHOP 2…

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LinkedOmics :: Data Download

RNAseq (HiSeq, Gene level, Tumor) Download RNAseq data RSEM upper-quartile normalized (Illumina HiSeq platform, Gene-level) gene Expression (RSEM-UQ, Log2(Val+1)) 140 28057 cct RNAseq (HiSeq, Gene level, Normal) Download RNAseq data RSEM upper-quartile normalized (Illumina HiSeq platform, Gene-level) gene Expression (RSEM-UQ, Log2(Val+1)) 21 28057 cct RNAseq (HiSeq, Gene level, Duct) Download…

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ggplot2 – adding a trend line in ggplot as well as ascertain its significance

I need help with finding and adding a trend line into my ggplot generated from an lmer model. My objective is to determine whether there is a significant trend within my exposure group, as well as to ascertain its significance. library(lme4) # linear mixed-effects models library(lmerTest) # test for linear…

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Line-type not matching legend in ggplot – General

I’m trying to plot two data.frames in a single plot, but for some reason the legend isn’t match my line-type that I’ve given it. Is there a more efficient way to do this? library(dplyr) library(ggplot2) library(Rmisc) black_line <- other %>% group_by(Month, Zone) %>% dplyr::summarise(q1=quantile(freq, probs = 0.25, na.rm = TRUE),…

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Detection of Plasmodium simium gametocytes in non-human primates from the Brazilian Atlantic Forest | Malaria Journal

WHO. World malaria report 2022. Geneva: World Health Organization; 2023. Google Scholar  Ministério da Saúde/Secretaria de Vigilância em Saúde. Malária 2021. Boletim Epidemiológico. Número especial. Brasília: MS/SVS; 2021. 100 pp. Melo JO, Padilha MAO, Barbosa RTA, Alonso WJ, Vittor AY, Laporta GZ. Evaluation of the malaria elimination policy in Brazil:…

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Handling NA’s in Deseq2

Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…

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Endophytic bacterial diversity by 16S rRNA gene sequencing of Pak choi roots under fluazinam, Trichoderma harzianum, and Sophora flavescens inoculation

Ahemad M, Khan MS (2012) Effect of fungicides on plant growth promoting activities of phosphate solubilizing Pseudomonas putida isolated from mustard (Brassica compestris) rhizosphere. Chemosphere 86(9):945–950. doi.org/10.1016/j.chemosphere.2011.11.013 Article  CAS  PubMed  Google Scholar  Al-Askar AA, Saber WI, Ghoneem KM, Hafez EE, Ibrahim AA (2021) Crude citric acid of Trichoderma asperellum: tomato…

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featurecounts not working on mirbase annotation file

featurecounts not working on mirbase annotation file 0 Hello I am trying to analyze miRNA-seq data but I am having problems with the mapping. I always get pretty much 0 counts with the built in annotation file, so I got one from miRBase. However, I always get an error when…

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Metagenomics Databases for Bacteria | SpringerLink

Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685 CrossRef  CAS  PubMed  PubMed Central  Google Scholar  Bharti R, Grimm DG (2021) Current challenges and best-practice protocols for microbiome analysis. Brief Bioinform 22:178–193 CrossRef  CAS  PubMed  Google Scholar  Human Microbiome Project, C (2012) A framework…

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Backcrossing to different parents produced two distinct hybrid species

Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinforma 12:246. doi.org/10.1186/1471-2105-12-246 Article  Google Scholar  Anderegg WRL, Flint A, Huang C-Y, Flint L, Berry JA, Davis FW et al. (2015) Tree mortality predicted from drought-induced vascular damage. Nat Geosci 8:367–371 Article  CAS  Google Scholar …

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r – What is causing my ggplot2 boxplot to turn into skinny lines instead of wide boxes using the width argument?

I am struggling with boxplots in R studio. I have a data set that looks like this: Site date Chloride_mgL B 2021-06-08 12:00:00 29.13800 D 2021-06-08 12:00:00 29.41100 D 2021-06-15 12:00:00 29.92400 E 2021-06-08 12:00:00 29.29100 A 2021-06-08 12:00:00 29.16800 D 2021-06-22 12:00:00 32.79500 C 2021-06-22 12:00:00 30.59200 Site is…

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Analysis of tRNA-derived small RNAs

Introduction Sarcoidosis is a multisystem inflammatory disease of unknown aetiology that is characterised by non-caseating epithelioid granulomatous lesions (aggregates of lymphocytes, macrophages, epithelioid cells, and giant cells).1 Typical clinical features include bilateral hilar lymph node lesions, pulmonary infiltration, and eye and skin lesions. Some patients may also have neurological and…

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Genetic determinants of Biofilm formation of Helicobacter pylori using whole-genome sequencing | BMC Microbiology

Correa P, Houghton J. Carcinogenesis of Helicobacter pylori. Gastroenterology. 2007;133(2):659–72. Article  CAS  PubMed  Google Scholar  Dube C, Tanih N, Ndip R. Helicobacter pylori in water sources: a global environmental health concern. Rev Environ Health. 2009;24(1):1–14. Article  CAS  Google Scholar  Stark RM, Gerwig GJ, Pitman RS, Potts LF, Williams NA, Greenman…

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Matthew Nilo, New Jersey lawyer, arrested in connection with Charlestown rapes

The former resident of the North End is accused of sexually assaulting four women in the Terminal Street area on Aug. 18, 2007, Nov. 22, 2007, Aug. 5, 2008, and Dec. 23, 2008, Boston police Commissioner Michael Cox said Tuesday. “All four cases are DNA connected,” Cox said. Matthew J….

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ggplot2 – Spatial Interpolation Map Temperature using ggplot in R

I would like to create 3 maps of spatial interpolation of a country (like belgium) using the GADM geopkg data that can be found there : gadm.org/download_country.html. The idea would be to create 3 interpolated maps : Voronoi interpolation IDW interpolation Ordinary Kriging interpolation I also would like to use…

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r – Annotating only unique duplicated key values on a diverging bar chart in ggplot2

Say I have a dataframe (df) with a total of 2 columns and 40 rows. The first column have duplicated key/ID values and the second contains 20 positive values, followed by 20 negative ones. Because of this, I decided to go for a diverging bar chart. But whenever I plotted…

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ggplot2 – Change order of bars and stacks in stacked barplot (R)

This question already has answers here: Closed 23 hours ago. I´m trying to graph a series of 11 variables from 5 groups in a stacked barplot. This is my data and code inf_source <- structure(list(inf_episode = c(“First”, “Second”, “Third”, “Fourth”, “Fifth”), Pneumonia = c(16,6,2,0,0), IAI =…

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ggplot2 – How can you compress the view of a graph in R Studio? (having trouble seeing data after shrinking x and y axis and changing fill color)

Running this code was successful: POP_data %>% ggplot(aes(x = year, y = average_POP, )) + geom_col(color = “blue”, width = .7, alpha =1) + labs(title = “Average Total Population From 2000 to 2015”, x = “Year”, y= “Average Total Population (in thousands)”) Just as some background, I ran the following…

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Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut | BMC Genomics

Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol Mol Biol Rev. 2017;81(4):e00036–17. Stewart CJ, Ajami NJ, O’Brien JL, Hutchinson DS, Smith DP, Wong MC, et…

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the monitor in mcallen, texas obituaries

If you are interested in reading The Monitor McAllen Texas obituaries, you can find them online or in the print edition of the newspaper. Learn About Online Memorials 269 talking about this. I was honored to have known Jeannie while living and growing up in McAllen. Mrs. Stroud, may you…

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Classification problem with GPT-3.5-turbo-model in Rstudio (sentiment analysis) – API

Hi! Currently trying to do a sentiment analysis with GPT-3.5-turbo-model in Rstudios, where my goal is to categorise each data row as either positive, negative or neutral. I have created a limited dataset with 50 rows, for which I have tried to create a loop that categorises 10 rows at…

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ZNF330/NOA36 interacts with HSPA1 and HSPA8 and modulates cell cycle and proliferation in response to heat shock in HEK293 cells | Biology Direct

Cell lines, culture conditions, heat shock treatment and transfections HeLa, HEK293 and 2D12 (a NOA36-knockout HEK293-cell line generated in this work) cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 100 U/mL penicillin and 100 µg/mL streptomycin at 37 °C in a CO2 incubator. For heat…

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rstudio – How can I create new columns with developmental stage duration based on previous columns in r?

I have a data frame that represents animal development over time. I have columns with treatments and species then many columns representing days. It looks like this: df <- data.frame (Species = c(“sp1”, “sp1”, “sp2”), Treatment = c(“hot”, “cold”, “hot”), Apr1 = c(“egg”, “egg”, “egg”), Apr2 = c(“1”, “egg”, “1”),…

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Solved ggplot (data(), aes (x = factor(Financial_status )))+

My Question to Chegg Expert. #################################################################install.packages(“caret”)install.packages(“corrplot”)install.packages(“caTools”)install.packages(“rpart.plot”)install.packages(“ggplot2”)################################################################# Loading Necessary Libraries #########################################################rm(list = ls())library(tidyverse)library(dplyr)library(ggplot2)library(tidyr)library(caret)library(rpart)library(corrplot)library(caTools)library(rpart.plot)library(e1071) ################################################################# Loading dataset set and Simple EDA ####################################################### # Loading the datasetlibrary(readr)dataset <- read_csv(“dataset.csv”)View(dataset) # summary of the datasetsummary(dataset) # checking null valuescolSums(is.na(dataset)) # structure of the datasetstr(dataset) ################################################################# dataset Cleaning ####################################################################### # Function to get modegetmode <-…

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r – How can I arrange a bar plot using ggplot2 based on the distribution proportions of variables?

I’m looking for a way to arrange the bar plot produced with ggplot2 by descending order of “utsugds2gp_22(happy condition)” that equal to 1 (category=not happy) within each scode1_22 group (area). The original bar plot I generated is below: My codes are as following : fill <- c(“white”, “#E1B378”) ka %>%…

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r – ggplot2 stacked column: How do I sort by date, use custom colors and change the legend?

Separately these seem easy, but I can only complete two of the requirements before breaking the third. What I want to do with a stacked column chart: Group by week and order the stacked bar chart with the earliest date (Thursday) on the bottom and the last date (Wed) on…

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Converting RefSeq protein accession IDs into entreZ IDs

Converting RefSeq protein accession IDs into entreZ IDs 0 Hi, I have a list of genes with Refseq accession ids and I want to convert it to EntrezID, which can then be fit in the GENE ONTOLOGY enrichment and pathway analysis like DAVID and gProfile (these IDs belong to a…

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Deep exome sequencing identifies enrichment of deleterious mosaic variants in neurodevelopmental disorder genes and mitochondrial tRNA regions in bipolar disorder

GBD 2016 Disease Injury Incidence Prevalence Collaborators. Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet. 2017;390:1211–59. Article  Google Scholar  Kato T. Current understanding of bipolar disorder:…

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Chemical Equations Balanced on 05/29/23

Balance equation of any chemical reaction online for freeNO2 + H2O = HNO3 + NO =>3 NO2 + H2O = 2 HNO3 + NO (NH4)2CO3 = NH3 + H2O + CO2 =>(NH4)2CO3 = 2 NH3 + H2O + CO2 NaOH + H3PO4 = Na3PO4 + H2O =>3 NaOH + H3PO4…

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Add lines to the legend in R and ggplot2

I’m trying to make a map in R (ggplot2 and sf) but I can’t seem to add transport lines to the legend. I have 4 lines (T1, T2, T3, T4) whose size I can’t change either. I also can’t manage to add a background map like OSM or a light…

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r – adjusting row height in ggplot lollipop

I need some help formatting my lollipop graph. The rows are too far apart from each other, with too much white space in each row therefore the top and bottom lines are too close to the edges of the plot. Ive tried adjusting a few formatting things in the plotting…

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Concepts & Syntax | Intro to R and RStudio (beginner)

1. Operators In R, an operator is a special symbol or keyword used to perform operations on one or more values. There are several types of operators in R, including: Assignment Operators: These operators are used to assign a value to a variable. Examples include <- and =. Arithmetic Operators:…

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r – How to Resolve Warning Message in lme4 mixed effects model?

I am having an issue with running a linear mixed effects model. I’m constantly presented with the same warning message and I’m unsure how to go about tackling this issue. The code: model_CRP <- lmer(mem ~ binding*time_years + AGE + GENDER + EDU_VERHAGE_YEARS + (1 | famnr) + (1+time_years|famnr:EMI), data=df_long_final,…

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DownsampleSam

I am trying to run DownsampleSam with Picard version: 2.26.5 on the following script and i get an error about Provider GCS. code: import os,sys from multiprocessing import Pool # the original depth of NA12878 and YH-1 nadepth=812.40 yhdepth=407.25 work_dph=int(sys.argv[1]) napercent = [0.99,0.95,0.90,0.80,0.70,0.60] yhpercent = [0.01,0.05,0.10,0.20,0.30,0.40] #yhpercent = [0.05] NAtotal=”/media/marina/marina2TB/BIOFILES/bams/na.addRG.mdup.bam”…

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How to process (seems) Agilent microarrry data?

Edit September 5, 2019 NB – this original answer is for 1-colour (channel) Agilent data. Another generic pipeline for 2-colour Agilent is here: A: build the expression matrix step by step from GEO raw data ————— Limma can be used to process Agilent microarray data. Assuming that your data is…

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Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives

Abstract Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein…

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Takeda and HUTCHMED Announce New Drug Application NDA for Fruquintinib for Treatment of Previously Treated Metastatic Colorectal Cancer Granted Priority Review

Shanghai, China & Hong Kong & Osaka, Japan & Cambridge, Mass., Florham Park, N.J., United States:   − Prescription Drug User Fee Act (PDUFA) Target Action Date Set for November 30, 2023 − NDA Includes Results From the Phase 3 FRESCO-2 and FRESCO Clinical Trials …

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R+ggplot2+facet_wrap: preserve the with of the bars

Please have a look at the reprex at the end of the post. It is a faceted barchart where the bars are placed in decreasing order in each subplot. My only question is how to ensure that the bars have the same consistent width in all the subplots. I had…

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Solved For the above Table 1 , We have created a entire

For the above Table 1 , We have created a entire datapipeline code in R language as below. <!– ## R Markdown –> <!– This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R…

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R Basics: Quick and Easy – Easy Guides – Wiki – STHDA | Quick Start

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

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Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds

Asalone KC, Ryan KM, Yamadi M, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR (2020) Regional sequence expansion or collapse in heterozygous genome assemblies. PLoS Comput Biol. doi.org/10.1371/journal.pcbi.1008104 Article  PubMed  PubMed Central  Google Scholar  Bankevich A, Nurk S,…

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Assigned taxonomy after dada2 only “NAs” or “Mitochondria”

Hi, I followed the dada2 tutorial on 16S and ITS amplicon metagenomic data from soil samples. However, when trying to assign a taxonomic rank to my ASV table using DECIPHER, I only get “NAs”. When using the dada2 native’s Bayesian method, I get “NA” or “Mitochondria” (family). For my 16S…

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Solved THIS IS AN R PROGRAMMING PROJECT.IMPORTANT: DO NOT

Transcribed image text: Questions: In order to answer each question, please write your own function without using barplot(), hist() or boxplot() and etc. functions in r-project or r-shiny or ggplot , hand in the r functions and outputs. Please do not copy and paste any function from internet; if you…

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Bug#1036718: unblock: slurm-wlm-contrib/22.05.8-4

Package: release.debian.org Severity: normal User: release.debian….@packages.debian.org Usertags: unblock X-Debbugs-Cc: oliv…@na.icar.cnr.it Please unblock package slurm-wlm-contrib This release provide the same version level of the free package slurm-wlm [ Reason ] This package has no change, this transition is only needed to align its version to the main version of the package…

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Single-Molecule Imaging of Lateral Mobility and Ion Channel Activity in Lipid Bilayers using Total Internal Reflection Fluorescence (TIRF) Microscopy

This protocol describes how to use TIRF microscopy to track individual ion channels and determine their activity in supported lipid membranes, thereby defining the interplay between lateral membrane movement and channel function. It describes how to prepare the membranes, record the data, and analyze the results. Ion channels are not…

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How to add a geom_bar layer with a stat of summary to an error bar plot? – tidyverse

library(tidyverse) library(palmerpenguins) p <- penguins %>% tidyr::drop_na() %>% ggplot(aes(x = species, y = body_mass_g)) + geom_errorbar(stat = “summary”, fun.data = \(x) mean_se(x, 1.96), width = 0.1) + expand_limits(y = 0) p p + geom_bar(stat = “summary”, fun.data = \(x) mean(x)) #> Error in `geom_bar()`: #> ! Problem while setting up…

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Bug#1036717: unblock: slurm-wlm/22.05.8-4

Package: release.debian.org Severity: normal User: release.debian….@packages.debian.org Usertags: unblock X-Debbugs-Cc: oliv…@na.icar.cnr.it Please unblock package slurm-wlm This release simply fix Breaks/Replaces deps and reintroduce a configuration file removed accidentally [ Reason ] This release will ensure a smoother update from bullseye [ Impact ] No impact is expected [ Tests ] Although…

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Growth Medium 1S – Nordic Biosite

Additional Information This liquid Growth Medium is a complete medium optimized to culture select BPS Bioscience cell lines. Optimized for Use With: CRISPRa (SAM) HeLa Cell Line (BPS Bioscience, #78193), CRISPRa (SAM) HepG2 Cell Line (BPS Bioscience, #78194) Article No BPS-78221 Country Availability SE, FI, DK, NO, IS, EE, LV,…

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The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae

Elston KM, Leonard SP, Geng P, Bialik SB, Robinson E, Barrick JE. Engineering insects from the endosymbiont out. Trends Microbiol. 2022;30:79–96. Article  CAS  PubMed  Google Scholar  Brophy JAN, Triassi AJ, Adams BL, Renberg RL, Stratis-Cullum DN, Grossman AD, et al. Engineered integrative and conjugative elements for efficient and inducible DNA…

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[Solved] I am building a decision tree model in R (rstudio) with the dataset…

I am building a decision tree model in R (rstudio) with the dataset attached but have gotten this error “Error in train_violence(violence$class ~ ., data = train_violence, method = “rpart”,  :  could not find function “train_violence” when i run it. i have the train_violence function already created so i do…

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r – plot data on stacked bar chart in ggplot2

Is this your desired output? library(tidyverse) library(ggnewscale) df <- read.table(text = “ID Genus name value 1 JP Dermatophagoides GroupA 0.997 2 JP Dermatophagoides GroupB NA 3 JP ‘Dermatophagoides evansi’ GroupA 0.00259 4 JP ‘Dermatophagoides evansi’ GroupB NA 5 AM ‘Dermatophagoides farinae’ GroupA 0.302 6 AM ‘Dermatophagoides farinae’ GroupB 0.303 7…

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Phase 1 trial to model primary, secondary, and tertiary dengue using a monovalent vaccine | BMC Infectious Diseases

Messina JP, Brady OJ, Golding N, Kraemer MUG, Wint GRW, Ray SE, Pigott DM, Shearer FM, Johnson K, Earl L, et al. The current and future global distribution and population at risk of dengue. Nat Microbiol. 2019;4(9):1508–15. Article  CAS  PubMed  PubMed Central  Google Scholar  Zeng Z, Zhan J, Chen L,…

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ggplot2 (1) (pdf) – Course Sidekick

Ggplot2-Rtitle: “Analysis Indian population”# by: “Bommareddy leela Sravanthi,20012467”# Output: pdf_document.## IntroductionIndia, often known as the Republic of India, is a South Asian nation. It is the world’s mostpopulous democracy, the second-most populated nation by area, and the seventh-largestnation overall. Its land borders with Pakistan to the west, China, Nepal, and…

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r – ggplot with points in left reversed y axis and bars in secondary axis

I’m trying to have a ggplot with two vertical axes to be produced in different ways depending on user selection. One selection lets the user reverse each axis. Another selection lets them select between points and bars for the series in each axis. I’m having issues when the main (left-side)…

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Error to executing the Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R – Community Plugin Support

Hello all,I’m trying to follow the tutorial cited and I ran the first steps but I’m having problems running the command:gplots::venn(list(metadata=metadata$SampleID, shannon=shannon$SampleID)) with the error: Error in metadata$SampleID : object of type ‘closure’ is not subsettable and the command: metadata %>% filter(!is.na(shannon)) %>% ggplot(aes(x=TIME, y=shannon, color=SAMPLES)) + stat_summary(geom=”errorbar”, fun.data=mean_se, width=0)…

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r – Setting the axes of a ggplot scatterplot to manually line up with geom_rect elements

I’m trying to make a scatter plot with a log scale that has 3 geom_rect() features laying out different “bins” for some density features. Whenever I add the geom_rect() features, it increases the limits of the x and y axis. Ideally, I’d like the rectangles to line up with the…

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Dupilumab Reduces COPD Exacerbations for Patient with T2 Inflammation in Landmark Phase 3 Trial

©pascalkphoto/Adobe Stock In the phase 3 BOREAS clinical trial study of patients with chronic obstructive pulmonary disease (COPD) and type 2 inflammation, those treated with dupilumab (Dupixent) experienced fewer COPD exacerbations, improved lung function, better health-related quality of life, and less severe symptoms compared with patients given a placebo. The findings were published in…

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Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients

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

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r – ggplot – how to draw a perfect diagonal line?

There are three limits that you might want to use. The plot corners (green points); The last breaks (red points); The actual xlim’s and ylim’s (blue points). “1.” Can be achieved with Allan’s annotation_custom answer. For “2.” and “3.” we must extract the limits and breaks. This can be done…

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r – How to deal with time series data to create new x and y axis lines to ggplot graph?

I’m trying to present a ggplot graph similar to Base R graphs. The issue I have is dealing with time series data (date and time) to draw the x and y axis properly. I used the same approach provided by Baptiste to create an x and y axis function: R-style…

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r – facet_grid, extra unintended NA line in plot

I´m creating a plot using the facet_grid function of ggplot2 where every panel consists of a scatterplot with connected lines of 5 variables. My data can be found here. I used this code from the referred link to create the output below. library(tidyverse) library(ggplot2) p<-2.5 #PointSize lw<-0.7 #Lineweight plot_data %>%…

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R ggplot2: Weird x axis labels

I have a question concerning a plot. I have two datatables with the exact same type and structure. > dput(test_ok_score_per_week) structure(list(week = structure(c(14851, 14858, 14865, 14872, 14879, 14886, 14893, 14900, 14907, 14914, 14921, 14928, 14935, 14942, 14949, 14956, 14963, 14970, 14977, 14984, 14991, 14998, 15005, 15012, 15019, 15026, 15033, 15040,…

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Phase 3 Study Finds Dupilumab Reduces COPD Exacerbations in Patients With Type 2 Inflammation

In the phase 3 BOREAS study of patients with chronic obstructive pulmonary disease (COPD) and type 2 inflammation, those treated with dupilumab (Dupixent) experienced fewer COPD exacerbations, improved lung function, better health-related quality of life, and less severe symptoms compared with patients given a placebo. The findings were published in…

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Identifying signatures of positive selection in human populations from North Africa

Henn, B. M. et al. Genomic ancestry of North Africans supports back-to-Africa migrations. PLOS Genet. 8, e1002397 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Arauna, L. R. et al. Recent historical migrations have shaped the gene pool of Arabs and Berbers in North Africa. Mol. Biol. Evol. 34, 318–329…

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How to add conditional annotation from other column of R dataframe in ggplot2

I’m trying to make a plot from a dataframe of over 300k rows where the peaks and valleys will be annotated from another column rather than the x and y. How can I do that..!! Dataframe : chr start end.x StoZ.x Hscore end.y StoZ.y Tier Gene 1 chr1 1 10000…

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Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels

Dubilier N, Bergin C, Lott C. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Microbiol. 2008;6:725–40. Article  CAS  PubMed  Google Scholar  Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the dark: phylogenetic and physiological diversity of chemosynthetic symbioses. Annu Rev Microbiol. 2021;75:695–718….

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Immune-related transcripts, microbiota and vector competence differ in dengue-2 virus-infected geographically distinct Aedes aegypti populations | Parasites & Vectors

Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nature. 2013;496:504–7. Article  CAS  PubMed  PubMed Central  Google Scholar  Stanaway JD, Shepard DS, Undurraga EA, Halasa YA, Coffeng LE, Brady OJ, et al. The global burden of dengue: an…

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envfit with ggplot creates disproportionate arrows – General

Hello, I am trying to add envfit to my NMDS plot made in ggplot and my arrows are disproportionate to the plot, where the arrows are too small. Here is my code: df = read.csv(“df.csv”, header = TRUE) com = df[,10:11] #where columns 10 and 11 are my NMDS scores…

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r – How to customize y-axis intervals and marks in ggplot with limited intervals and 40 unit increments?

I am trying to make a ggplot, but I am not sure how to change the y-axis intervals or show specific intervals on the y-axis. How do you make the y-axis of a ggplot go up by 40, with the min being 40 and the max being 200, but only…

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Investigating the shared genetic architecture between schizophrenia and body mass index

Fleischhacker WW, Arango C, Arteel P, Barnes TR, Carpenter W, Duckworth K, et al. Schizophrenia-time to commit to policy change. Schizophr Bull. 2014;40:S165–S94. Article  PubMed  PubMed Central  Google Scholar  Cirulli ET, Guo L, Leon Swisher C, Shah N, Huang L, Napier LA, et al. Profound perturbation of the metabolome in…

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Precision Targeting of Na-K-2Cl cotransporter (NKCC1) RNA In Vitro with RfxCas13d

Abstract The Na-K-2Cl cotransporter (NKCC1) is considered an attractive drug target in the Central nervous system (CNS) for treating various CNS disorders. However, the specific role of NKCC1 in different types following injury within the CNS is not well understood due to its expression in multiple cell types. Additionally, there…

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Prevalence of mutations in the cysteine desulfurase IscS (Pfnfs1) gene in recurrent Plasmodium falciparum infections following artemether-lumefantrine (AL) and dihydroartemisinin-piperaquine (DP) treatment in Matayos, Western Kenya | Malaria Journal

WHO. Word Malaria Report 2021. Geneva: World Health Organization; 2021. Google Scholar  White NJ, Nosten F. Artemisinin-based combination treatment of falciparum malaria. Am J Trop Med Hyg. 2007;77(Suppl 6):181–92. PubMed  Google Scholar  Amato R, Pearson RD, Almagro-Garcia J, Amaratunga C, Lim P, Suon S, et al. Origins of the current…

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Solved In RStudio:1. How can you tell if an object is a

In RStudio: 1. How can you tell if an object is a tibble? (Hint: try printing mtcars, which is a regular data frame). My verbal response to 1 is: 2. (1 point) What function would you use to read a file where fields were separated with “|”? My verbal response…

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Can’t run Parallel inference

transformers version: 4.12.3 Platform: Darwin-20.6.0-x86_64-i386-64bit Python version: 3.7.0 PyTorch version (GPU?): 1.10.0 (False) Tensorflow version (GPU?): not installed (NA) Flax version (CPU?/GPU?/TPU?): not installed (NA) Jax version: not installed JaxLib version: not installed Using GPU in script?: No Using distributed or parallel set-up in script?: parallel Hi, I have warning…

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Whole genome sequencing of a novel chitinolytic Streptomyces sp. RB7AG reveals it’s chitosan production potential: optimization of the process through Taguchi experimental design

Adhikari HS, Yadav PN (2018) Anticancer activity of chitosan, chitosan derivatives, and their mechanism of action. Int J Biomater 2018:1–29 Google Scholar  Aider M (2010) Chitosan application for active bio-based films production and potential in the food industry. LWT-Food Sci Technol 43:837–842 CAS  Google Scholar  Ash K, Ramteke PW (2018)…

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Candidemia case caused by a drug-resistant Candida auris

Introduction Candida auris is a human fungal pathogen, first isolated in Japan in 2009.1 Since then, many C. auris isolates have been reported worldwide.2–4 This pathogen can contaminate the environment around the patients who were colonized by the fungus, and can survive for long periods in major outbreaks.5 Recent studies…

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Decoy In Reference Assembly

Decoy In Reference Assembly 2 I am using 1000 Genomes data with my new project. When I am inspecting the reference assembly they have been using, I found it contains a “decoy” contig. The 1000 Genomes FAQ says: For the final round of alignments the sequence data will be mapped…

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ggplot2 – How to make base R double barplot in ggplot

I’ve made the following double marplot in base R, but would like to make the same graph in gig-lot if possible. How would I go about doing this? data <- structure(list( A= c(53, 39), B = c(30, 36), C = c(12, 19), D = c(5, 6)), .Names = c(“Poor”, “Fair”,…

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ggplot2 – R: How to replace very significant p values with ‘p < 0.001'? ggplot / boxplot

I am looking for help to change the presentation of the p-value on the display in a boxplot. For now: var = different samples (blood etc.) group: sample.group (positive / negative).. When running the following code, I get a boxplot with a p-value. The p-value is 6.7e^-07, what I need…

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r – Order facets vertically rather than side-by-side in ggplot2

In this data: Example <- structure(list(PP_dur_cumsum = c(0, 18, 34, 50, 68, 84, 100, 118, 134, 150, 168, 184, 200, 218, 234, 250, 268, 284, 300, 318, 334, 350, 368, 384, 400, 418, 434, 450, 468, 484, 500, 518, 534, 550, 568, 584, 600, 618, 634, 650, 668, 684, 700,…

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Tracing the introduction of the invasive common myna using population genomics

Acclimatisation (6 January 1877) Southland Times. Page 2. paperspast.natlib.govt.nz/newspapers/ST18770105.2.7. Accessed 21 January 2022 Adamack AT, Gruber B (2014) PopGenReport: simplifying basic population genetic analyses in R. Methods Ecol Evol 5:384–387. doi.org/10.1111/2041-210x.12158 Article  Google Scholar  Andrews S (2010) FastQC. A quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc/ Andrews KR,…

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