Category: GPL

Bristol Myers Squibb hiring Senior Scientist, Translational Bioinformatics in Princeton, New Jersey, United States

At Bristol Myers Squibb, we are inspired by a single vision – transforming patients’ lives through science. In oncology, hematology, immunology and cardiovascular disease – and one of the most diverse and promising pipelines in the industry – each of our passionate colleagues contribute to innovations that drive meaningful change….

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The shape of the graph outputed by REVIGO is broken.

I’ve had the same problem recently! I think some publications just screenshot the default output. The rrvgo package can make a similar plot using the scatterPlot() function: www.bioconductor.org/packages/release/bioc/vignettes/rrvgo/inst/doc/rrvgo.html My own modified R-code based on revigo looks more like this (currently 🙂 ). There are three comments in there where you…

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H20 AutoML : kaggle

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Bullsquid game : gmod

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gromacs-plumed | MacPorts

Molecular dynamics package designed for simulations of proteins, lipids, and nucleic acids.: (THIS PORT INSTALLS A VERSION OF GROMACS PATCHED WITH PLUMED) GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed…

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Bioconductor – target

DOI: 10.18129/B9.bioc.target     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see target. Predict Combined Function of Transcription Factors Bioconductor version: 3.10 Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) . Extend…

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Pavlov is Gmod VR : PavlovGame

pavlov VR is better compared to what cs source was. some cool mods, but built around the “search and destroy” gamemode. in another separate point, an actual flexible script oriented modding game like Gmod would probably be an killer app in VR, in a similar way VRchat content is 99%…

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BioSpace hiring Bioinformatics Scientist in Gaithersburg, Maryland, United States

We are currently searching for a Bioinformatics Scientist to provide support to the National Institutes of Health (NIH). This opportunity is a full-time position with MSC, and it is on-site in Gaithersburg, MD. Duties & Responsibilities Work independently and collaboratively to develop or optimize procedures that improve the throughput of…

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unable to access index for repository https://bioconductor.org

Recently I have updated my mac, R, and R studio and the new versions are as follows: sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6 I have used DESEQ2without issue prior to the update. After the update, I need to re-install DESEQ2. For this…

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replica tool gun : gmod

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Sexy Gordon Freeman poster. : gmod

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BiocManager::install(“DNAcopy”) failed to install in r

Enter the body of text here Code should be placed in three backticks as shown below BiocManager::install(“DNAcopy”) # include your problematic code here with any corresponding output ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10) Installing package(s)…

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Colour UMAP based on expression of multiple genes

Hi all, I was just wondering if anybody had any experience with coloring something like a UMAP made in ggplot based on the expression of multiple genes at the same time? What I want to do is something like the blend function in Seurat featureplots, but with 3 genes /…

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GOChord plot problem when using the chor_dat function to create a matrix

GOChord plot problem when using the chor_dat function to create a matrix 0 Hello All, I am trying to create a GOChord plot for circular visualization of the results of gene- annotation enrichment analysis. I created all the data frames myself and cross-checked the types of every column in each…

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435.gromacs: SPEC CPU2006 Benchmark Description

435.gromacs: SPEC CPU2006 Benchmark Description Benchmark Name 435.gromacs Benchmark Author Erik Lindahl <lindahl [at] gromacs.org>Department of Structural BiologyStockholm Bioinformatics CentreStockholmSweden David van der Spoel <spoel [at] gromacs.org>Department of BiochemistryUppsala UniversityBox 576, 751 23 UppsalaSWEDEN Benchmark Program General Category Chemistry / Molecular Dynamics Benchmark Description 435.gromacs is derived from GROMACS, a…

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Bioconductor – esATAC

DOI: 10.18129/B9.bioc.esATAC     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see esATAC. An Easy-to-use Systematic pipeline for ATACseq data analysis Bioconductor version: 3.12 This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw…

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Errors : gmod

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Gedmatch help making sense? : 23andme

The oracle is telling you which of the reference populations this calculator (MDLP World-22) uses are the closest match to you; the closest matches would have admixture results closest to what you have. Single population is which reference population oracle thinks you’re closest to; in this case that’s Luiseño, though…

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GO BACK TO WORK!! : gmod

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Gmod Recon Soldier Art : gmod

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mdozmorov/excluderanges: Genomic coordinates of problematic genomic regions as GRanges

Genomic ranges of problematic genomic regions that should be avoided when working with genomic data. For human, mouse, and selected model organisms. TL;DR – For human hg38 genome assembly, Anshul recommends ENCFF356LFX exclusion list regions. BED files of exclusion regions are available on the ENCODE project website (Amemiya, Kundaje, and…

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Hello All, How can I cluster different GO_categories so that it does not look scattered as in my case?

Hello All, How can I cluster different GO_categories so that it does not look scattered as in my case? 0 The data frame is provided as an image: My R code is: Bubble_plot_5 <- read_excel(“GO_Bubble_plot.xlsx”, sheet = “GO_5”) view(Bubble_plot_5) ggplot(Bubble_plot_5, aes(y = reorder(GO_Term, as.numeric(GO_Category)), x = Gene_Count, size = Gene_Count))+…

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Gene Ontology Bubble Plot using ggplot2

So with your data that seems to look something like this: structure(list(GO_term = structure(c(2L, 4L, 3L, 1L), .Label = c(“Kinase”, “Metabolism”, “Nucleus”, “Photosynthesis”), class = “factor”), Number = c(5L, 10L, 15L, 16L), Class = structure(c(3L, 2L, 1L, 1L), .Label = c(“hs”, “hzs”, “start_duf”), class = “factor”), Type = structure(c(1L, 1L,…

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Bioconductor – ewceData (development version)

DOI: 10.18129/B9.bioc.ewceData     This is the development version of ewceData; for the stable release version, see ewceData. The ewceData package provides reference data required for ewce Bioconductor version: Development (3.14) This package provides reference data required for ewce. Expression Weighted Celltype Enrichment (EWCE) is used to determine which cell…

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Bioconductor – PWMEnrich

DOI: 10.18129/B9.bioc.PWMEnrich     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see PWMEnrich. PWM enrichment analysis Bioconductor version: 3.11 A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already…

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Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits

Significance Marine dissolved organic matter, which originates from phytoplankton, holds as much carbon as Earth’s atmosphere; yet, the biological processes governing its fate are primarily studied under idealized laboratory conditions or through indirect measures such as genome sequencing. In this work, we used isotope labeling to directly quantify uptake of…

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R Shiny volcano plot

R Shiny volcano plot 0 hello community, I want to generate a volcanoplot with a csv file ==> file1: gene;Id;log2FC;P-Value;P-Value-adj in my server : server <- function(input, output) { re <- reactive({ req(input$file1) data <- read.csv(input$file1$datapath, sep = “;”) return(data) }) output$table <- renderDataTable({ D <- re() DT::datatable(D) } )…

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R Shiny

R Shiny 0 hello community, I want to generate a volcanoplot with a csv file ==> file1: gene;Id;log2FC;P-Value;P-Value-adj in my server : server <- function(input, output) { re <- reactive({ req(input$file1) data <- read.csv(input$file1$datapath, sep = “;”) return(data) }) output$table <- renderDataTable({ D <- re() DT::datatable(D) } ) output$plot2<-renderPlot({ D…

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Florida Dark RP Gmod : BrandNewSentence

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interesting kaggle datasets

Kaggle ARC challenge has set May 27 as the final submission deadline for the ARC challenge. Kaggle Datasets. The internet is a treasure trove of valuable information for aspiring data scientists. • updated 2 years ago (Version 3) Data Tasks Code (1,473) Discussion (1) Activity Metadata. (Some might need you…

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Bioconductor – genotypeeval

DOI: 10.18129/B9.bioc.genotypeeval     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see genotypeeval. QA/QC of a gVCF or VCF file Bioconductor version: 3.10 Takes in a gVCF or VCF and reports metrics to assess quality of calls. Author: Jennifer Tom [aut, cre] Maintainer:…

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How to merge HMM files for HMMSearch?

I’m trying to add several mult-HMM files together but I haven’t had much luck. First I tried to just cat them, then I realized that it won’t work if there is an overlap of HMMs within the files. I then made a script that only concatenates unique ones but once…

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Bioconductor – rGREAT

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see rGREAT. Client for GREAT Analysis Bioconductor version: 3.2 This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user’s input and automatically retrieving…

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sc-RNA matrix appears to be empty

I’m trying to load the gene count sparse matrix from this source in R: oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/downloads However the matrix’s contents appear to be empty. To download I used wget on the command line: wget -O – shendure-web.gs.washington.edu/content/members/cao1025/public/mouse_embryo_atlas/gene_count.txt | head > data.txt And then load matrix like so: matrix <- Matrix::readMM(file=”~/scratch/rtrujillo/RNA-seq/sci-seq/data.txt”) To…

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Bioconductor – DMRScan

DOI: 10.18129/B9.bioc.DMRScan     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DMRScan. Detection of Differentially Methylated Regions Bioconductor version: 3.10 This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The…

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Frequency of the gene expression in Seurat

DotPlot computes the fraction of cells expressing a gene in each group (metadata column), so you can cheat a little and extract the results from it [source]. library(“Seurat”) features <- c(“PECAM1”, “CD14”) group_column <- “clusters” perc_exp <- DotPlot(seu, features=features, group.by=group_column)$data[, c(“features.plot”, “id”, “pct.exp”)] The returned data will look something like…

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conda stop to install or work

conda stop to install or work 1 Hi, I need help please I have Mac Bigsur conda suddenly stop working or installing or even uninstalling I believe that there’s an issue in the env. I’ve been tried many solutions but still the same ! conda install -c bioconda samtools Collecting…

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Bioconductor – MADSEQ

DOI: 10.18129/B9.bioc.MADSEQ     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MADSEQ. Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data Bioconductor version: 3.10 The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the…

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Bioconductor – Heatplus

DOI: 10.18129/B9.bioc.Heatplus     Heatmaps with row and/or column covariates and colored clusters Bioconductor version: Release (3.6) Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is…

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Bioconductor – ProteoDisco (development version)

DOI: 10.18129/B9.bioc.ProteoDisco     This is the development version of ProteoDisco; to use it, please install the devel version of Bioconductor. Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Development (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions…

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Reading microarray data from the Gene Expression Omnibus

Hi Caitlin, For this study, the uploaded data is normalised via GC-RMA, but is not log [base 2] (log2) transformed. To retrieve it, you need to do: library(GEOquery) gset <- getGEO(‘GSE12657’, GSEMatrix = TRUE, getGPL= FALSE) if (length(gset) > 1) idx <- grep(‘GPL8300’, attr(gset, ‘names’)) else idx <- 1 gset…

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Bioconductor – hgu95av2probe

DOI: 10.18129/B9.bioc.hgu95av2probe     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see hgu95av2probe. Probe sequence data for microarrays of type hgu95av2 Bioconductor version: 3.10 This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from www.affymetrix.com. The…

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Bioconductor – proteinProfiles

DOI: 10.18129/B9.bioc.proteinProfiles     Protein Profiling Bioconductor version: Release (3.6) Significance assessment for distance measures of time-course protein profiles Author: Julian Gehring Maintainer: Julian Gehring <jg-bioc at gmx.com> Citation (from within R, enter citation(“proteinProfiles”)): Installation To install this package, start R and enter: ## try http:// if https:// URLs are…

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Bioconductor – nethet

DOI: 10.18129/B9.bioc.nethet     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see nethet. A bioconductor package for high-dimensional exploration of biological network heterogeneity Bioconductor version: 3.11 Package nethet is an implementation of statistical solid methodology enabling the analysis of network heterogeneity from high-dimensional…

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HeatMap, problems with the scale color and dendrogram

HeatMap, problems with the scale color and dendrogram 1 Hi, I am trying to make a Heatmap of some analyzed RNAseq data. I am using ggplot2 with R. The problem I have is that I cannot see well the upregulated and the downregulated genes. I can’t get the colors shown…

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Bioconductor – BasicSTARRseq

DOI: 10.18129/B9.bioc.BasicSTARRseq     Basic peak calling on STARR-seq data Bioconductor version: Release (3.6) Basic peak calling on STARR-seq data based on a method introduced in “Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq” Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 10.1126/science. 1232542. Epub 2013 Jan 17. Author: Annika…

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Interpretation of DESeq2 results with 3 factorial design with interaction terms.

Assalam Alykom, I’m doing a 3 factorial DESeq2 analysis with interaction terms, I want to extract results to answer specific biological questions. Here is the code for the design: dds<-DESeqDataSetFromMatrix(countData = CountData, colData = metaData, design = ~ age + gender + viralLoad + age:viralLoad + gender:viralLoad) dds <- DESeq(dds)…

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All samples have 0 counts for all genes. check the counting script

DESeq2: All samples have 0 counts for all genes. check the counting script 1 @2f3f6904 Last seen 1 hour ago United Kingdom I am having problems importing my HTSeq count data- it tells me the counts are zero when this is clearly not the case when head outputs: >head(WTCHG_862660_71955267) GeneID…

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visualisation of proteomics data using r and bioconductor

R package version 0.99.7, 2014. [9] have developed an approach to estimate peptide isoelectric point values using a Support Vector Machine classifier from the caret package [10]. [73] De Duve, C., Beaufay, H., A Short History of Tissue Fractionation. The readers are referred to the respective documentation and vignettes for…

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Color layer in ggplot (Volcano plot)

Forum:Color layer in ggplot (Volcano plot) 0 I’m trying to plot a volcano plot with ggplot’s vplot. My issue is that I want the colored dots on the front layer rather than the back layer. Is there a way? For example: In the figure I want all the red dots to…

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Survival analysis with gene expression

[*] For this example, we will load GEO breast cancer gene expression data with recurrence free survival (RFS) from Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis. Specifically, we will encode each gene’s expression into Low | Mid | High based on…

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Plot average expression instead of -Log10(FDR/p-val) in volcano plot

Plot average expression instead of -Log10(FDR/p-val) in volcano plot 1 Hi guys, is there a way to plot the average expression of a list of genes on the y axis of a volcano plot instead of -log10(FDR/P-val) using EnhancedVolcano or another way (like ggplot2)? Thank you in advance plot volcano…

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genbank submission bankit

Submission of sequence data to NCBI archives . Learn more. This post will show you how to… Careers, General: your contact details, authors, publication, data release date, Original or third-party assembly/annotation, Set designation (if applicable) for multiple sequences of the same locus, Nucleotide sequences in FASTA or alignment format, Source…

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unable to fetch raw CEL files

GEOquery: unable to fetch raw CEL files 1 Dear all, I tried to access the raw data using getGEOSuppFiles (), but the untar () function did not return the necessary CEL files. Code used: ########### getGEOSuppFiles(“GSE59857”) setwd(“./GSE59857/”) untar(“GSE59857_RAW.tar”) ########### untar returned only the platform files: > dir() [1] “GPL10558_HumanHT-12_V4_0_R1_15002873_B.txt.gz” [2]…

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ncbi genbank submission

This document describes how to use the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus command line interface of the GenBank Submission Portal. Found inside – Page 4NCBI builds GenBank primarily from the submission of sequence data from authors and from the bulk submission of expressed sequence tag (EST), genome…

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Scientist, Bioinformatics/Computational Biology Job Opening in Cambridge, MA at Flagship Pioneering, Inc.

About Inzen:    Inzen Therapeutics is a privately held, early-stage biotechnology company exploring Thanokine Biology as a surprising and vital driver of disease.  While the ability of living cells to respond to messages from other living cells is a well-established concept, Inzen has identified that living cells also respond to messages released by cells as they undergo turnover and…

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Intellia Therapeutics to Present at Chardan’s 5th Annual Genetic Medicines Conference

CAMBRIDGE, Mass., Sept. 27, 2021 (GLOBE NEWSWIRE) — Intellia Therapeutics, Inc. (NASDAQ:NTLA), a leading clinical-stage genome editing company focused on developing curative therapeutics using CRISPR/Cas9 technology both in vivo and ex vivo, will present at Chardan’s 5th Annual Genetic Medicines Conference on Monday, October 4, 2021 at 10:30 a.m. ET….

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Plot genes derived from time course experiment as line graph

Plot genes derived from time course experiment as line graph 0 Hi! I would like to plot the log2FC of 80 genes of a time course experiment (from 0 to 168hrs) as line plot. So originally my dataset has the genes in rows and the log2FC per time point in…

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Bioconductor – LineagePulse

DOI: 10.18129/B9.bioc.LineagePulse     This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see LineagePulse. Differential expression analysis and model fitting for single-cell RNA-seq data Bioconductor version: 3.7 LineagePulse is a differential expression and expression model fitting package tailored to single-cell RNA-seq data (scRNA-seq). LineagePulse…

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Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_

Result for: Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_ Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_ GitHub – rbberger/lammps-doc-utils: Utilities for … Fri, 27 Aug 2021 01:36:00 GMT – This tool is no longer necessary. All of the LAMMPS documentation…

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Bioconductor – seqCAT

DOI: 10.18129/B9.bioc.seqCAT     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see seqCAT. High Throughput Sequencing Cell Authentication Toolkit Bioconductor version: 3.9 The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and…

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Bioconductor – Melissa

DOI: 10.18129/B9.bioc.Melissa     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Melissa. Bayesian clustering and imputationa of single cell methylomes Bioconductor version: 3.9 Melissa is a Baysian probabilistic model for jointly clustering and imputing single cell methylomes. This is done by taking…

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Bioconductor – PREDA

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see PREDA. Position RElated Data Anlysis Bioconductor version: 3.0 Package for the position related analysis of quantitative functional genomics data. Author: Francesco Ferrari <francesco.ferrari at unimore.it> Maintainer: Francesco Ferrari <francesco.ferrari at unimore.it> Citation (from…

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Bioconductor – netprioR

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see netprioR. A model for network-based prioritisation of genes Bioconductor version: 3.4 A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from…

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Bioconductor – xps

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see xps. Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays Bioconductor version: 2.9 The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays,…

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Adding multiple timepoint on dumbbell plot

Hi, I am in the process of plotting a dumbbell with ggplot2 and (ggalt). Attaching thr dumy data and R code. I am unable to add any of the third time point, but can add 1 and 2, 2 and 3 and 3 and 1. The plot should be sorted…

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Bioconductor – Dune

DOI: 10.18129/B9.bioc.Dune     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see Dune. Improving replicability in single-cell RNA-Seq cell type discovery Bioconductor version: 3.11 Given a set of clustering labels, Dune merges pairs of clusters to increase mean ARI between labels, improving replicability….

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Problem with minfi package

I have problem with “getGEO” part of this tutorial and i get “.rowNamesDF” error : kasperdanielhansen.github.io/genbioconductor/html/minfi.html >geoMat <- getGEO(“GSE174818”) Found 1 file(s) GSE174818_series_matrix.txt.gz Using locally cached version: C:UsersMahyaAppDataLocalTempRtmpsz3t0D/GSE174818_series_matrix.txt.gz Rows: 0 Columns: 129 0s– Column specification ——————————————- Delimiter: “t” chr (129): ID_REF, GSM5331993, GSM5331994, GSM5331995, GSM53319… i Use spec() to retrieve…

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Bioconductor – eisa

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see eisa. Expression data analysis via the Iterative Signature Algorithm Bioconductor version: 2.9 The Iterative Signature Algorithm (ISA) is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular)…

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Paths and timings of the peopling of Polynesia inferred from genomic networks

1. Low, S. Hawaiki Rising: Hōkūle‘a, Nainoa Thompson, and the Hawaiian Renaissance (Univ. of Hawaii Press, 2019). 2. Kirch, P. V. On the Road of the Winds (Univ. of California Press, 2017). 3. Mulrooney, M. A., Bickler, S. H., Allen, M. S. & Ladefoged, T. N. High-precision dating of colonization…

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Flavivirus-GLUE by giffordlabcvr

Overview The flaviviruses (family Flaviviridae) are a group of enveloped, positive-strand RNA viruses, many of which pose serious risks to human health on a global scale. Arthropod-borne flaviviruses such as Zika virus (ZIKV), Dengue virus (DENV), and yellow fever virus (YFV) are the causative agents of large-scale outbreaks that result…

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Bioconductor – rgsepd

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see rgsepd. Gene Set Enrichment / Projection Displays Bioconductor version: 3.4 R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential…

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Bioconductor – flagme

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see flagme. Analysis of Metabolomics GC/MS Data Bioconductor version: 2.9 Fragment-level analysis of gas chromatography – mass spectrometry metabolomics data Author: Mark Robinson <mrobinson at wehi.edu.au> Maintainer: Mark Robinson <mrobinson at wehi.edu.au> Citation (from…

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TCGA dataset normalization

TCGA dataset normalization 0 hi. i am new to machine learning. i want to normalize my data which I downloaded from UCSC Xena browser for pancreatic cancer TCGA PAAD is its id. when I try to run this code it is showing error given below library( “DESeq2” ) library(ggplot2) countData…

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Don’t play “dodge the bullets” with Pedguin!

I can just about hear Rythian in my head shouting “stop running and just shoot him!” I just watched that episode earlier, and that exchange sort of gets a bit painful. Rythian: “Oh man, Ben tried to run away instead of shooting again.” Ben: “I didn’t have a gun.” Rythian:…

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Problem with Risk table in Kaplan-Meier plot

Hi everybody! It is my first time here and I wish to as clear and kind as every user in this forum. I am trying to generate a Kaplan-Meier Plot for Overall Survival using survival and ggplot2 packages, with the data contained in data1. OS variable codifies time variable and…

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miRNAs and mRNAs in intestinal ischemia-reperfusion injury

Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…

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Create violin plot with specific value label that corresponding to graph

Example data. # Counts df <- as.data.frame(sapply(seq(2, 10, 2), function(x) rnorm(10, x, 1))) colnames(df) <- paste0(“group_”, 1:5) df$val <- paste0(“val_”, 1:10) > df group_1 group_2 group_3 group_4 group_5 val 1 0.4267759 4.599173 6.256323 8.534080 12.778423 val_1 2 2.9344611 3.649858 7.141283 9.299478 10.735906 val_2 3 0.8156248 3.363994 7.285855 7.503840 9.755979 val_3…

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hypothetical protein DAPPUDRAFT_213302, maker-scaffold2255_size18018-snap-gene-0.6 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of hypothetical protein DAPPUDRAFT_213302 vs. L. salmonis genes Match: EMLSAG00000000401 (supercontig:LSalAtl2s:LSalAtl2s1063:86108:87342:-1 gene:EMLSAG00000000401 transcript:EMLSAT00000000401 description:”maker-LSalAtl2s1063-snap-gene-0.46″) HSP 1 Score: 149.443 bits (376), Expect = 4.121e-44Identity = 91/196 (46.43%), Postives = 119/196 (60.71%), Query Frame = 0 Query: 14 MDKITDLQVEPLT–NSRFVKPLRLRFKQDGKVKVWDLIQCHASVAVVIFNQTTQKFVFVRQFRPAVYFSALRRAQGDVEPGTQFKGDEIDPKVGITLELCAGIVD-KSKSLIEIAHEEILEETGYDVPMNLIEEIQTFPVGVGVGGENMTLFCAEVTEAMRKGPGGGLAEEGEMIDVIEMGVEETRTLMRAKSVT 206 MDK+ VEPL +SRFV P R+ ++Q+G…

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Bioconductor – GeneGA

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see GeneGA. Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm Bioconductor version: 2.9 R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure…

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Bioconductor – Harman

DOI: 10.18129/B9.bioc.Harman     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Harman. The removal of batch effects from datasets using a PCA and constrained optimisation based technique Bioconductor version: 3.12 Harman is a PCA and constrained optimisation based technique that maximises the…

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Bioconductor – ERSSA

DOI: 10.18129/B9.bioc.ERSSA     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ERSSA. Empirical RNA-seq Sample Size Analysis Bioconductor version: 3.9 The ERSSA package takes user supplied RNA-seq differential expression dataset and calculates the number of differentially expressed genes at varying biological replicate…

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Bioconductor – NBAMSeq

DOI: 10.18129/B9.bioc.NBAMSeq     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see NBAMSeq. Negative Binomial Additive Model for RNA-Seq Data Bioconductor version: 3.9 High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step…

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