Tag: NA

ggplot2 – How to wrap graphs by categories while keeping the same width of bars with ggplot in R?

I am struggling with using facet_grid() and facet wrap() with ggplot(). I would like to be able to wrap the different stacked barcharts for every two categories (of the variable Department here) but at the same time have the same width of bars. The first action can be achieved with…

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Plotting date intervals in ggplot2

I have a dataset which has a bunch of date intervals (i.e. POSIXct format start dates and end dates). In the example provided, let’s say it’s each period is associated to when someone was in school or out of school. I’m interested in plotting the data in ggplot2, each row…

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Writing ggplot custom geometry function

stat_accum <- function(mapping = NULL, data = NULL, geom = “point”, position = “stack”, …, show.legend = NA, inherit.aes = TRUE) { layer( data = data, mapping = mapping, stat = StatAccum, geom = geom, position = position, show.legend = show.legend, inherit.aes = inherit.aes, params = list( na.rm = na.rm,…

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ggplot2 – R knitr Markdown: Output Plots within For Loop

I am using child Rmd files in markdown, also works in sweave. in Rmd use following snippet: “`{r run-numeric-md, include=FALSE} out = NULL for (i in c(1:num_vars)) { out = c(out, knit_child(‘da-numeric.Rmd’)) } “` da-numeric.Rmd looks like: Variabele `r num_var_names[i]` ———————————— Missing : `r sum(is.na(data[[num_var_names[i]]]))` Minimum value : `r min(na.omit(data[[num_var_names[i]]]))`…

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how to make 2d rendering on directx 11 more faster – Graphics and GPU Programming

I make an editor for own game engine and I used for 2d rendering Direct2D but I wanted to render a directx texture on window in editor, I didn’t find convenient way to convert directx texture to direct2d bitmap. I decided to make own 2d render on directx 11 and…

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Heatmap deseq2

I’m using deseq2 for DEA but when I create a heatmap with only DEGs, it looks very strange: I’m not sure whether there are only overexpressed genes or whether the dataset is not normalized properly. I probably made a mistake somewhere in my coding but I don’t know where to…

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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Figure.03

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Change size of label annotations in a ggplot

I am trying to change text label sizes inside my plot (not the axes, rather the label annotations) I am working with a phyloseq object but I don’t think that matters. Here is the code and the output. Any suggestions? plot_ordination(prokaryote_ra, ordBC, color = “Stage”, label=”SampleID”) + ggtitle(“PCoA: Bray-Curtis”) graph…

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Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

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Monocle3 differential expression failed when active.assay is not “RNA”

after run estimate_size_factors, data with active.assay = ‘integrated’ works too, but no deg in the result. > [email protected] = ‘integrated’ > cds_raw <- as.cell_data_set(seurat_object) Warning: Monocle 3 trajectories require cluster partitions, which Seurat does not calculate. Please run ‘cluster_cells’ on your cell_data_set object > cds <- cluster_cells(cds_raw) > pr_graph_test_res <-…

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python – NameError: name ‘Seq’ is not defined

I want to fill null value with Average. data2 = data.na.drop(Seq(“code”)).select(avg(col(“code”))) data2.display() This error I got: ————————————————————————— NameError Traceback (most recent call last) <command-1060196488305723> in <module> —-> 1 data2 = data.na.drop(Seq(“code”)).select(avg(col(“code”))) 2 data2.display() NameError: name ‘Seq’ is not defined Read more here: Source link

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Change log2FoldChange range – plotMA

You can use base R graphics to make these plots. The data is sitting there in columns of the res object, so you can filter it directly, and use boolean vectors to pick out the things you need: # make sure there are no NA values sum(is.na(res$log2FoldChange)) # choose some…

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[forlilab/Meeko] PDBQT tree error

[x] I believe this to be a bug with Meeko resulting from OpenBabel issue #2433. I report it here because Meeko has the same error. Environment Information Operating system and version: Centos 7.4 Expected Behavior Example 1. C1(NC2=NC(C3=CN=CC=C3)=CC=N2)=CC=CC=C1 As for example 1 molecule, obabel give a PDBQT file with 2…

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GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

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R ggtree: How to label single tree tip with ggtree similar to labeling nodes with geom_cladelabel

I’m having trouble with labeling single tips in my tree with ggtree. I’m trying to highlight and label nodes from a tree with geom_hilight and geom_cladelabel. This seems to work fine with nodes that have more than 1 tree tip, but when I try to label a single tip, I…

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ggplot2 – R ggplot – ploting multiple variables with sub-categories in the same plot with two axes

I have this data: date area people_tested positive_cases positive 2021-12-09 Total 76282.0 402.0000 0.005300000 2021-12-10 Total 84023.0 389.0000 0.004600000 2021-12-09 Total_3da NA 382.3333 0.004900000 2021-12-10 Total_3da NA 377.6667 0.004933333 2021-12-09 Paris_3da 75257.4 NA NA 2021-12-10 Paris_3da 71553.6 NA NA and I would like to create a plot with a line…

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faq – What should I do when my neural network doesn’t learn?

There’s a saying among writers that “All writing is re-writing” — that is, the greater part of writing is revising. For programmers (or at least data scientists) the expression could be re-phrased as “All coding is debugging.” Any time you’re writing code, you need to verify that it works as…

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Microarray analysis and functional prediction of differentially expressed circular RNAs in acquired middle ear cholesteatoma | BioMedical Engineering OnLine

1. Castle JT. Cholesteatoma pearls: practical points and update. Head Neck Pathol. 2018;12(3):419–29. Article  Google Scholar  2. Xie S, Wang X, Ren J, Liu W. The role of bone resorption in the etiopathogenesis of acquired middle ear cholesteatoma. Eur Arch Otorhinolaryngol. 2017;274(5):2071–8. Article  Google Scholar  3. Bhutta MF, Williamson IG,…

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10q26 FGFR2 Break Apart FISH Probe Kit

1 0q26 FGFR2 Break Apart FISH Probe Kit For Research Use Only Not for Use in Diagnostic Procedures 0q26 FGFR2 Break Apart FISH Probe Kit 09N /R2 Key to Symbols Used 09N /R2 Reference Number Lot Number Global Trade Item Number Centromere D0S294 0q26. Region FGFR2 5 ATE SHGC-529 Telomere…

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Adrenal aldosterone-producing adenoma | IJGM

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

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Chitosan Nanoparticles for Antiviral Drug Delivery

Introduction According to research conducted in many labs in the field of nanotechnology, particularly in nanomedicine, it appears that nanotechnology and nanomedicine should play an active role in treating and preventing the spread of Coronavirus Infectious Disease-19 (COVID-19).1–6 Polymeric nanoparticles, such as chitosan NPs,7 are one of the possibilities available…

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r – How to draw boxplot by multiple groups using ggplot2?

I try to get a boxplot with the following specifications for the following variables: assets, liability. My data is firms financial statement and firms are classified big and small firms (categorical variable lbg30). Time (years) is also categorized by two period pre-crisis and post-crisis (categorical variable postcrisis). So I want…

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ggplot: remove lines at ribbon edges

You can remove the border using the colour argument: ggplot(d, aes(Time, y, color = Object, fill = Object)) + geom_line(size = 2) + geom_ribbon(aes(ymin = lower, ymax = upper), alpha = .3, colour = NA) geom_ribbon understands linetype aesthetic. If you want to map linetype to a variable include it…

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python – How to get the Cumulative Distribution Function with PyMC3?

I am trying to recreate the models in John Kruschke’s ‘Doing Bayesian Data Analysis‘ and am currently trying to model ordinal data (chapter 23 in the book. This is the JAGS model that I’m trying to recreate: total = length(y) #Threshold 1 and nYlevels-1 are fixed; other thresholds are estimated….

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r – How to avoid too much space around polar chart in ggplot

This is my dataframe: my_df <-structure(list(Statistic = c(“Shots on target %”, “Shots on target %”, “% of dribblers tackled”, “% of dribblers tackled”, “Ground passes”, “Ground passes”, “Passes Completed”, “Passes Completed”, “Live-ball passes”, “Live-ball passes”, “Passes Attempted (Right)”, “Passes Attempted (Right)”, “Passes Attempted”, “Passes Attempted”, “Successful Pressure %”, “Successful Pressure…

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shade alternate days with POSIXct timestamp data

I can plot a line of a variable vs timestamp (plot p1 below). However, I’d like to shade the plot for alternate days. The data has an entry once an hour for two days. dat <-structure(list(TIMESTAMP = structure(c(2L, 3L, 14L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 4L, 5L, 6L,…

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Merge and Perfectly Align Histogram and Boxplot using ggplot2

since yesterday I am reading answers and websites in order to combine and align in one plot an histogram and a boxplot generated using ggplot2 package. This question differs from others because the boxplot chart needs to be reduced in height and aligned to the left outer margin of the…

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r – ggplot2 vertical colorbar title right centered

Here is a solution, inspired in this SO post.Note that in the question you have fill = guide_colourbar(.) when it should be colour = guide_colourbar(.). library(ggplot2) ggplot(df, aes(x=img_type, y=metric),show.legend = FALSE) + geom_point(aes(size = abs_corr, colour=corr))+ scale_size(range =c(-0.1,20) )+ scale_colour_gradient2( low = “#7e1952”, high = “#2f7a9a”, space = “Lab”, na.value…

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[Solved] Having two RStudio instances running GRASS simultaneously

for (roads_r in rasters){ # roads_r is a rasterized lines object, value 1 where roads, rest is NA # built a random name (I’m aware I could use tempdir(), but explored this to have files at hand tmp_custom <- paste0(“tmp”, paste0(sample(1:9, 1), sample(1:9, 1), sample(1:9, 1), sample(1:9, 1))) tempDir <-…

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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…

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Frontiers | The cGAS-STING Pathway: A Promising Immunotherapy Target

Introduction Invaded by exogenous or endogenous pathogens, the host immune system will be activated accordingly to resist harm and maintain homeostasis, which includes innate immunity and adaptive immunity. As the first line of host immune defense, innate immunity plays a critical role in recognizing extracellular and intracellular pathogens (1, 2)….

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raster – Explicit temp files in rgrass7 / fasterRaster to avoid interferences when running simultaneous R sessions

I’m finding errors using the function fasterRastDistance() in the fasterRaster R library when running the same script in several simultaneous RStudio instances. The error looks like this: ERROR: You must select the PERMANENT mapset before updating the current location’s projection (current mapset is <<UNKNOWN>>) access: Invalid argument ERROR: LOCATION <C:/Users/JavierF/AppData/Local/Temp/RtmpqoyKjm<UNKNOWN>>…

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NA values for mitochondrial gene percentage

NA values for mitochondrial gene percentage 0 I am running Seurat on publicly available dataset of ~400k cells. More than 80% of the cells are returned as NA when I use percentageFeatureSet(object, pattern = “^MT-“). How should I interpret these result? Does this mean the 80% of cells are of…

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Tanzania Independence Day 2021: Google Doodle celebrates Tanzanian Republic Day

Google Doodle observes Tanzania Independence Day, which is additionally now and then alluded to as ” Republic Day,” on December 9, 2021. This public holiday is always celebrated on December 9th. The day celebrates the finish of British rule in Tanganyika in 1961. It was on this day in 1961…

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r – Position Trend line regression equation in ggplot

i am trying to plot trend lines equation with R square for three variable (SA,SA1,SA2) using ggplot geom_smooth(). While plotting three variables i get overlapping equation. I tried to adjust the y lab position using stat_regline_equation(label.y = c(1.78e15,3.9e17,2.5e15)) but miserably failed in doing so. DATA LINK (Requirement: 3 trend lines…

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AYUSH_MALAKAR_HW6.doc – Course IST 687 Assignment HW 6 Name Ayush Malakar Date library’ggplot2#including package#Step-1 AQ_dataset

################################################ Course: IST 687# Assignment: HW 6# Name: Ayush Malakar# Date: 08/17/2021# ###############################################library(‘ggplot2’) #including package#Step-1AQ_dataset<- airquality #loading the dataset into a new variable#Step-2AQ<- na.omit(AQ_dataset) #removing NA’s from the dataset#Step-3 (1)#1x <- ggplot(AQ, aes(x=Ozone)) #defining plot and aestheticsx<- x+geom_histogram(bins =5, colour=’black’, fill=’white’) # defining the shape and structure of the histogramx…

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AYUSH_MALAKAR_HW9.doc – Course IST 687 Assignment HW 9 Name Ayush Malakar Date#library library”kernlab library”ggplot2 library”e1071

############################################### # Course: IST 687 # Assignment: HW 9 # Name: Ayush Malakar # Date: 09/09/2021 # ############################################### #library library(“kernlab”) library(“ggplot2”) library(“e1071”) library(“gridExtra”) #Step 1: Load the data airquality #replacing NA’s with mean values airquality$Ozone[is.na(airquality$Ozone)] <- round(mean(airquality$Ozone, na.rm = TRUE)) airquality$Solar.R[is.na(airquality$Solar.R)] <- round(mean(airquality$Solar.R, na.rm = TRUE)) airquality #Step 2: Create…

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Error while converting Gene ID to Ensembl IDs

I have a DEGs data frame with Gene IDs. Pic for reference below I am trying to convert the Gene_IDs into Ensembl IDs. I have tried the following methods library(“AnnotationDbi”) library(“org.Hs.eg.db”) res3$ensid = mapIds(org.Hs.eg.db, keys=res3$Gene_ID, column=”ENSEMBL”, keytype = “SYMBOL”, multiVals = “first”) The above code converted most of the gene…

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R how to correct for multiple comparisons in ggplot correlations?

I have the following dataset: structure(list(Age_group = structure(c(4L, 2L, 2L, 2L, 4L, 2L, 2L, 4L, 3L, 1L, 2L, 1L, 1L, 4L, 1L, 2L, 1L, 4L, 3L, 4L, 4L, 1L, 2L, 2L, 1L, 2L, 1L, 3L, 3L, 2L, 2L, 3L, 4L, 3L, 2L, 4L, 2L, 2L, 3L, 4L, 4L, 4L, 1L,…

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r – ggplot: multiple time periods on same plot by month

I am trying to plot multiple time-periods on the same time-series graph by month. This is my data: pastebin.com/458t2YLg. I was trying to avoid dput() example but I think it would have caused confusion to reduce the sample and still keep the structure of the original data. Here is basically…

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‘Deprecated’ Error with ngs.plot.r after sys admin update Bioconductor

Loading R libraries…..Done Configuring variables… Using database: /home/yensin/software/ngsplot/database/hg19/hg19.ensembl.genebody.protein_coding.RData Done Analyze bam files and calculate coverageWarning message: ‘isNotPrimaryRead’ is deprecated. Use ‘isSecondaryAlignment’ instead. See help(“Deprecated”) ………………………………………………………………………………………………………………………………………………………………………………….Done Plotting figures…Error in seq.default(min.e, max.e, length.out = ncolor + 1) : ‘from’ cannot be NA, NaN or infinite Calls: plotheat -> ColorBreaks -> seq ->…

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How to extract genomic upstream region of a protein identified by its NCBI accession number?

How to extract genomic upstream region of a protein identified by its NCBI accession number? 1 I have a list of NCBI protein accession numbers. I would like to extract out the upstream genomic region of the corresponding gene’s nucleotide sequence. I will be thankful to you if you can…

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iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

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IRE combined with toripalimab versus IRE alone for LAPC

Introduction Pancreatic ductal adenocarcinoma (PDAC) is a lethal gastrointestinal disease with increasing morbidity, which also has a growing impact on cancer-specific mortality worldwide.1 Nearly 40% of all PDAC cases are localized to the pancreas and characterized with the involvement of major vascular structures, leading to unresectable disease without metastases detected…

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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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extract p-value from Tukey test and put in a Table.

Hi, I need to get in a list the values of p adj of multiple comparisons from Tukey test. I report the part of the script that gives me problems: for (i in 1:1293) { p_adjs = rep(NA, 1293) p_adjs = matrix(p_adjs, nrow=1293, ncol=6) if (sum(is.na(matrixDataLog[i,]))<3) { tukey = TukeyHSD(anova)…

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protti source: R/fetch_alphafold_prediction.R

#’ Fetch AlphaFold prediction #’ #’ Fetches atom level data for AlphaFold predictions either for selected proteins or whole #’ organisms. #’ #’ @param uniprot_ids optional, a character vector of UniProt identifiers for which predictions #’ should be fetched. This argument is mutually exclusive to the code{organism_name} argument. #’ @param…

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pandas – DataFrame to CSV save error on Kaggle Python. How to solve?

I’m trying to save a dataframe containing 20 million rows to a CSV format, with this: df_merge.to_csv(‘processed.csv’) After executing the code, I got this error message: OSError: [Errno 30] Read-only file system: ‘processed.csv’ What is this and how can I handle it? NOTE: The code is run on kaggle. Complete…

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Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Peptides are mapped onto PDB structures or AlphaFold prediction based on their positions. This is accomplished by replacing the B-factor information in the structure file with values that allow highlighting of peptides, protein regions or amino acids when the structure is coloured by B-factor. In addition to simply highlighting peptides,…

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Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas

Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 CAS  PubMed  PubMed Central  Article  Google Scholar  Alexander DH, Shringarpure SS, Novembre J, Lange K (2015) Admixture 1.3 software manual. UCLA Hum Genet Softw Distrib, Los Angeles Google Scholar  Angert AL, Bontrager…

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Combining RNA-Seq read counts from 2 lanes of the same sample (.txt file)

Hi, I have a question on combining read counts from 2 lanes of the same sample. I have a very large RNA-Seq dataset downloaded from the NCBI GEO. The data files are in the *.txt format and each sample with 2 lanes obtained from featureCounts. I would like to perform…

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gmod advanced duplicator 2

Advanced Duplicator 2 is a Garry’s Mod addon which implements a tool similar to the Duplicator, but with many added features. Yeah no problem mate, thanks for the response. I’m done with gmod and I don’t take requests, so please stop spamming the comment section. “Originally published in single magazine…

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What to do if the Entrez id that I have had been updated with a new one and now is associated with a gene

What to do if the Entrez id that I have had been updated with a new one and now is associated with a gene 0 For context, this is part of an RNAseq analysis, I have a list of genes, which was generated by annotateMyIDs using the Entrez id from…

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desEQ2 eRROR

I have count matrix from feature count with gene_names for each sample. When I am using DESeqDataSetfromMatrix with the following commands: count <- read.csv(“matrix.count”, header = TRUE, row.names = 1, sep =’t’) info <- read.table(“coldata2.txt”, header = TRUE, sep =’t’) library(DESeq2) library(apeglm) ds <- DESeqDataSetFromMatrix(count, info, ~condition) Error: DESeqDataSet(se, design…

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Genomic and phenotypic characteristics for Vibrio vulnificus

Background Fisheries and aquaculture are becoming increasingly intensive to meet recent human consumption, resulting in proliferation of marine pathogens and food security concerns.1,2 Vibrio species, as one of the most dangerous foodborne pathogens, cause vibriosis in human around the world.3 It has been reported that vibriosis resulted in 80,000 illnesses…

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Introducing NA by coercion error message when running pathfindR

Since the weekend I’ve been getting an “NAs introduced by coercion” error message when i run the pathfindR package. An example of some of my data is Gene.symbol <- c(“ACAA2”, “ACADVL”, “ACAT1”, “ACOT9”, “ACOX1”, “ADH5”, “AKR1A1”) logFC <- c(“3.3”, “3.9”, “1.5”, “1.7”, “2.4”, “1.9”, “1.7”) adj.P.Val <- c(“0.02”, “0.03”, “0.02”,…

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Gromacs: Class Members – Variables

Gromacs: Class Members – Variables   – n – N : t_UmbrellaWindow , t_bb n : t_coordselection , t_methoddata_kwreal , t_methoddata_permute , t_partition , gmx_fft_fftpack , t_spheresurfacebin , t_methoddata_kwint n_alloc : t_spheresurfacebin n_at_lam : df_history_t n_dev : gmx_gpu_info_t n_dev_compatible : gmx_gpu_info_t nalloc : cu_atomdata , cl_atomdata , gmx_ana_selvalue_t , swap_compartment…

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Outliers on DESEq2 Results

I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from 10 to 12, with a few counts > 9000. I process this data in Deseq2 and get that the gene is differentially expressed across several samples of interest. What can…

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The result of plink –freq is filled with NA

The result of plink –freq is filled with NA 0 I downloaded the vcf file. Then I used plink to convert it to a bed file and calculated the array frequency. However, the result of plink –freq was filled with NA. Can anyone give us an opinion? command ① ./plink –vcf…

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Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed  Google Scholar  2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS  PubMed  PubMed Central  Google Scholar  3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…

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how to analyse the correlation between two datasets (corr.test and corrplot)

Hi. I am Newbie in R. I am facing the problem of corr.test analysis. Actually, I would like to clarify the correlation between two different vectors ( Bacteria types versus environment factors). Then, I would like to plot a graph like this: There are two dataset for my analysis, here’s…

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GIAB Benchmark (High Confidence) Bed Filles

GIAB Benchmark (High Confidence) Bed Filles 0 Hi all, I havent used Genome in a Bottle for a couple of years. When I did use it, I recall I would download samples in VCF format for: AshkenaziTrio (three each) NA12878 (only one) ChineseTrio (three each) I would then download what…

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[Hands-on for beginners] Read kaggle’s “Predicting Home Prices” line by line (Part 2: Checking Missing Values)

Click here for the first content This is the second part of a project to make a note of the contents of hands-on, in which everyone will challenge the famous “House Price” problem of kaggle. It’s more of a memo than a commentary, but I hope it helps someone somewhere….

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network analysis for microbial amplicon sequencing data

Hello, I need to do microbial network analysis to identify the hub taxa and want to compare overall network properties. For this; I already calculated cor value and p-value in R by using the below codes, but I am not sure after this how to use igraph and how to…

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Analysing Microarray Data In Bioconductor

I was thinking about creating a tutorial on how to do a simple microarray analysis in Bioconductor. But, I realized this has already been done quite nicely at the Bioinformatics Knowledgeblog. Their first tutorial on the subject covers installation of necessary packages, downloading of cel files, describing the experiment, loading…

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Need help to remove NA values from data frame

Need help to remove NA values from data frame 2 I have this data frame : and I want to remove those rows which contain NA values from the log2fold change column How can I do this through R? DeSEQ2 R • 256 views Hi Anas, If your data frame…

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Getting cDNA sequence from NCBI

Getting cDNA sequence from NCBI 1 I am looking at NCBI’s api page and I cannot seem to find any endpoint that returns the cDNA by transcript id. In fact NCBI nuccore has a webpage for this. and if I want to i can scrape the part coming after ORIGIN….

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Determining the microbial and chemical contamination in Ecuador’s main rivers

Bacterial contamination in urban areas of the main Ecuadorian rivers All rivers showed E. coli levels above standard concentrations for bathing-water recommended by the USA, European and Brazilian guidelines (Fig. 1), in concordance with other studies in Latin America, such as Colombia34, Mexico4, and Perú35. Most of the rivers in this…

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Link between amino acid and a range of common diseases could help predict personal risk – Wellcome Sanger Institute

  Researchers have identified a link between mitochondrial DNA variants, amino acid fMet, and a range of common, late-onset diseases One of the first population-scale studies on how common genetic traits are influenced by variations in the DNA of mitochondria, the powerhouses of human cells, has been completed by scientists…

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Changing colour labels of samples with pheatmap

Bit of an R newbie here. I’m trying to generate a figure to see how RNA-seq samples are grouping via hierarchical clustering. Using this code rld<-vst(dds, blind=TRUE) rld_mat<- assay(rld) rld_cor<-cor(rld_mat) head(rld_cor) pheatmap(rld_cor,annotation = meta) heat.colors<-brewer.pal(9, “Blues”) annotdf<-data.frame(row.names = rownames(rld_cor)) pheatmap(rld_cor, annotation=meta, color=heat.colors, annotation_colors = ColorCode, border_color = NA, fontsize =…

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qualimap2 mean mapping quality

qualimap2 mean mapping quality 0 I’ve done a contrast experiment to see the difference between the bam with BQSR and the bam without BQSR. I use qualimap to evaluate both bams. This is the confusing part. Using hap.py and the giab na12878 truth vcf, shows the bam with BQSR is…

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Environmental Factor – September 2021: Intramural Papers of the Month

IntramuralBy Nicholas Alagna, Kelley Christensen, Mimi Huang, Janelle Weaver, and Qing Xu DNTP develops whole-genome sequencing of cell-free DNA in blood Researchers from the Division of the National Toxicology Program have developed a protocol for whole-genome sequencing of low quantities of circulating cell-free DNA. Small amounts of DNA are typically…

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DESeq2 analysis example, opinions?

Hello everyone, Purpose of the analysis: In there a difference between TOV21G-PacR and TOV21G-cont, and between the PacR and cont? My question is if this analysis makes sense for you? I am analyzing this particular gene set (GSE172016). Within the data there are two cell lines (“OVCAR3” and “TOV21G”) and…

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Modification of endoglin-targeting nanoliposomes | IJN

Introduction Today, malignant tumors (cancer) still severely imperil human health and cause millions of global mortality rates.1,2 Deep-seated solid tumors are challenging to cure by most therapeutic tools, mainly blamed on the complex tumor microenvironment (TME).3,4 Adoptive cell therapy (ACT), as one of the effective immunotherapeutic means for cancer treatment,…

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Extract multiple times a fasta sequence from a list by name

Hi everybody! I have uploaded on R a list of 9K fasta sequences, on which 40K SNPs map to – which means, some sequence host 1+ SNP. I have a R object (and a vcf as well) with the fasta sequences names and the SNP positions and I want to…

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Could amino acid finding from Cambridge scientists help predict our personal risk of common diseases?

Inside our cells are mitochondria, which act as their powerhouses – generating about 90 per cent of the energy required for the biochemical reactions required for them to function. This is just one of the vital biological functions of these organelles, which are unique in having their own genetic code….

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The association of amino acids with various common illnesses can help predict an individual’s risk

Mitochondria.Credits: Wikipedia Commons One of the first population-scale studies on how common genetic traits are affected by changes in mitochondrial DNA, the driving force of human cells, was the European Molecular Biology Laboratory at the Wellcome Trust Sanger Institute, University of Cambridge, EMBL. Tokoro (EMBL-EBI) and its collaborators. The team…

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How to combine a data frame with another data frame containing comma-separated values?

For dataframe manipulation, in general, you should look into the dplyr and tidyr packages, they offer endless possibilities if you learn to manipulate them (lots of practice will help). A good and concise cheatsheet is available here. Regarding this problem in particular, something like this should work: library(dplyr) library(tidyr) dfA…

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Handle inflated log2FC while using interaction term in DESeq2

Hi guys, I’m working with a 8 samples experiment (lower than 3x replicates, I know..) with a design like > colData(dds) DataFrame with 8 rows and 2 columns condition traitment <factor> <factor> 4200-JS-1 norm ctrl 4200-JS-2 norm ctrl 4200-JS-3 norm trt 4200-JS-4 norm trt 4200-JS-5 hyper ctrl 4200-JS-6 hyper ctrl…

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Link between amino acid and a range of common diseases could help predict personal risk

Mitochondria.Credits: Wikipedia Commons One of the first population-scale studies on how common genetic traits are affected by changes in mitochondrial DNA, the driving force of human cells, was the European Molecular Biology Laboratory at the Wellcome Trust Sanger Institute, University of Cambridge, EMBL. Tokoro (EMBL-EBI) and its collaborators. The team…

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Dealing with missing values in population allele frequency data in classifier model bulding context

Hi Stars, I would appreciate it if you share your inputs on the following issue: I am trying to make binary classifier models to classify variants into tow diffrent classes. The dataset is an annotated variant file with dimensions as 187,643 x 203. The first column contains class labels with…

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It’s not easy to pronounce. But one thing is certain about FDA-approved Comirnaty: It works

The Food and Drug Administration on Monday issued full authorization for the Pfizer-BioNTech COVID-19 vaccine. Soon, millions of Americans will face a confusing, difficult task: How in the heck do you pronounce Comirnaty? That’s the brand name for the Pfizer-BioNTech COVID-19 vaccine. And it’s pronounced “co-MER-na-tee” according to Scott Piergrossi,…

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Circos plot with logfold change RNA seq data

I am new to circos plot analysis and have been trying to use the cyclize package. I want to display mRNA differential gene expression data based on data analyses of 8 libraries and links between their respective target genes. The dataset I am working with looks like this geneid baseMean…

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Combining 2 different depth RNA-seq data (DESeq2)

Hello, I have two RNA-seq data generated from Illumina Novaseq (same experimental design but different depth, 25M and 15M reads/sample for Run1 and Run2 respectively). The dateset look like this: Samples Condition Run Sample_1 A R1 Sample_2 B R1 Sample_3 A R1 Sample_4 B R1 Sample_5 A R1 Sample_6 B…

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How to extract plots from ConsensusClusterPlus package

Hello All, Is there a way to extract the plots separately from the ConsensusClusterPlus package? For example, using the example data from the package, I can print the last three plots as below, library(ALL) data(ALL) d=exprs(ALL) mads=apply(d,1,mad) d=d[rev(order(mads))[1:5000],] d = sweep(d,1, apply(d,1,median,na.rm=T)) library(ConsensusClusterPlus) par(mfrow=c(1,3)) title=tempdir() results = ConsensusClusterPlus(d,maxK=6,reps=50,pItem=0.8,pFeature=1, title=title,clusterAlg=”hc”,distance=”pearson”,seed=1262118388.71279) But,…

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Combining RNA-seq data from 2 experiments (DESeq2)

Hello, I have two RNA-seq data generated from Illumina Novaseq (same experimental design but different depth, 25M and 15M reads/sample for Run1 and Run2 respectively). The dateset look like this: Samples Condition Run Sample_1 A R1 Sample_2 B R1 Sample_3 A R1 Sample_4 B R1 Sample_5 A R1 Sample_6 B…

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Positive selection population identification using xpehh

Positive selection population identification using xpehh 1 I am using Rehh package for identification of positively selected genes from our study. I am using the following script but confused with right reference. ies2xpehh( scan_pop1, scan_pop2, popname1 = NA, popname2 = NA, min_nhaplo = NA, standardize = TRUE, include_freq = FALSE,…

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Agilent-016436 Human miRNA Microarray 1.0

Upon request, a quick tutorial for processing the Agilent micro-RNA (miRNA) microarray data of GSE28955. The raw TXT files are contained in: ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28955/suppl/GSE28955_RAW.tar Download this TAR file Unpack it [the TAR file] Unzip the txt.gz files Store these [txt files] in a directory raw/ Then, create a tab-delimited file, targets.txt,…

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Discriminant gene analysis

Discriminant gene analysis 0 I want to obtain the top 5 discriminant genes (positive and negative direction) after a feature selection process. Is this the proper way to obtain the top 5 discriminant genes? # New data.frame with genes that have passed both (Fold and rawp) tests true.genes <- subset(gene.info,…

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lfcShrink probelm in many 0 count genes RNA-seq data

Hi, Dr love. I post a question about weird MAplot or volcano plot of DESeq2 diff result and also in biostar. ATpoint give a useful answer about too many 0 count genes and prefiltering. It seems that too many 0 count genes makes lfc shrink have a probelm. And I…

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weird MAplot or volcano plot of DESeq2 diff result

Hi, every one. I find a werid MAplot or volcano plot of DESeq reuslt. I am wondering whether you can give me some advice. This diff result is from two cell type bulk RNA-seq. I use two specific marker to get these two cell type using Flow cytometer. I alreadly…

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Variant Calling Heterozygous Reference Alleles

I am going to be working with VCF files a lot in the near future so I thought I would brush up on the practice. After much reading and research, there’s something that I just can’t wrap my head around. 1) In a diploid organism, you have 2 alleles for…

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Answer: PopGenome – VCF, fasta, GTF and codons still missing

Dear Maciek Hopefully you were able to solve these problems already. I cannot comment on the main set of issues you reported. However, I also encountered the error: `Error in START[!REV, 3] : incorrect number of dimensions` following certain instances of `set.synnonsyn` which I also noticed occurred for genes which…

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MAKER genome annotation error with SNAP ab initio prediction

I am trying to do a second round of maker genome annotation with ab initio prediction by snap. The error I am getting is as follows: error: unknown command “genome.hmm”, see ‘snap help’. ERROR: Snap failed –> rank=NA, hostname=bioinformatics ERROR: Failed while preparing ab-inits ERROR: Chunk failed at level:0, tier_type:2…

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How to colour points in cnetplot of clustprofiler?

I have a cnetplot from running enrichment with kegg using clusterprofiler. I have scores input as the fold change but for each gene in the plot they are not varying in colour to show their difference in the fold change score. My dataset is genes of entrez IDs and then…

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How to search dbSNP using a list of SNPs and retrieve Gene name (hgnc symbol if existing, otherwise just whatever is in there)

How to search dbSNP using a list of SNPs and retrieve Gene name (hgnc symbol if existing, otherwise just whatever is in there) 2 I have a list of 500.000 SNPs from which I want to obtain the gene name. I try to search with biomaRt library(data.table) library(biomaRt) rs <-…

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microarray miRNA expression data analysis

I wrote a script on how to analyze the microarray-based miRNA expression data. Here is my code: # general config baseDir <- ‘.’ annotfile <- ‘mirbase_genelist.tsv’ setwd(baseDir) options(scipen = 99) require(limma) # read in the data targets <- read.csv(“/media/mdrcubuntu/46B85615B8560439/microarray_text_files/targets.txt”, sep=””) # retain information about background via gIsWellAboveBG project <- read.maimages(targets,source=”agilent.median”,green.only…

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