Tag: R

Randomize Read Order In Multigbp Fastq File?

Randomize Read Order In Multigbp Fastq File? 3 Is there any method to randomize the read order in a multi-Gbp fastq file? fastq • 6.0k views Assuming you are talking about a single-end file, you can use awk to put each 4-line fastq entry on a single line. You then…

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Heatmap by group in R

Dear colleagues, Could you clarify please how to make such a figure with the help of ggplot2? I saw a similar solution, but I don’t understand how to properly reorder columns and rows… I created a test table. Group Name Sample1 Sample2 Sample3 A Sub 200 500 600 A Res…

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Two treatment regimens improve quality of life among patients with DLBCL

February 01, 2023 1 min read Source/Disclosures Published by: Source: Friedberg J, et al. Poster 2949. Presented at: ASH Annual Meeting and Exposition; Dec. 10-13, 2022; New Orleans. Disclosures: Friedberg reports no relevant financial disclosures. ADD TOPIC TO EMAIL ALERTS Receive an…

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Create Bivariate Visualizations In R Using ggplot2

Creating visualizations in R using ggplot2 can be a powerful way to explore and understand your data. One common type of visualization is the bivariate plot, which allows you to examine the relationship between two variables. In this tutorial, you’ll learn how to produce bivariate visualizations in R using ggplot2….

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Data Science Engineer – Government, Structures, Modelling, Math, Python, Java, Keras, PyTorch

Role: Data Science Engineer Contracting Authority: Government Contract Length: 1 Year Location: London IR35: Inside Pay Rate: Competitive Daily Rate Clearance: DV Clearance   An exciting opportunity has become available with our prestigious client who is a prominent government department. The client is seeking an experienced Data Science Engineer to join their welcoming team.   The Data…

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Error in .call.graphics(C_palette2, .Call(C_palette2, null)) : Invalid Graphics State

Error in .Call.graphics(C_palette2, .Call(C_palette2, NULL)) : invalid graphics state might occur while using the ggplot2 package. Its possible reasons include an incorrectly installed ggplot2 package, a messed up graphics device, insufficient plot area, etc. But there isn’t anything to worry about while you have this comprehensive guide opened up in…

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r – How can I make the labels more readable in this lollipop plot?

I am trying to make a lollipop plot that includes a text ‘condition’ and a value associated. The issue I am having is that, because there is so much data, the labels overlap. Is there an easy fix for this? This is my code (and my issue): library(ggplot2) df <-…

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Senior Data Scientist, Translational Bioinformatics Job

Job Description Who we are: Calico (Calico Life Sciences LLC) is an Alphabet-founded research and development company whose mission is to harness advanced technologies and model systems to increase our understanding of the biology that controls human aging. Calico will use that knowledge to devise interventions that enable people to…

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rstudio – Pathway to directory lost in R studio

I am relatively new to R studio, I am attempting to import a .RNK file to run on GSEA. However, the pathway to my working directory is lost and I keep receiving a file, “rt” warning message. When comparing my working directory with my usual windows explorer file, the files…

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Mesoblast Resubmits Biologic License Application (BLA) to FDA for Remestemcel-L in Children With Steroid-Refractory Acute Graft Versus Host Disease (Sr-aGVHD)

Validation of Remestemcel-L Potency Assay used in the Phase 3 Trial which Measures In-Vivo Activity based on Mechanism of Action Assay Identifies High-Potency Product Lots Associated with Enhanced Survival New Data Show that Remestemcel-L Improves Inflammatory Biomarkers and Survival in Children at Highest Risk of Mortality New 4-Year Data from…

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r – Connecting geom_line with dodged points within a point grouping, within a facet_wrap

Edit2: You could create an extra column with the x-axis position in numeric way to have the values dodged. You could use two x aesthetic columns for both the layer and geom_point and geom_line. Using scale_x_continuous to have the continuous axis to dodge the values and create labels like this:…

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pb with str_count – Posit Forum (formerly RStudio Community)

Here’s what I get on my install, a System76 version of Ubuntu 22.04 with version details as shown, using your example and the stringr help(str_count) examples. All appears as it should. What is very odd is that one or both of the two arguments, both shown as strings, which are…

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Trem2 H157Y increases soluble TREM2 production and reduces amyloid pathology | Molecular Neurodegeneration

Generation, genotyping, and off-target analysis of Trem2 H157Y knock-in mice Trem2 H157Y knock-in mice were generated via CRISPR/Cas9 by the Hope Center Transgenic Vectors Core of the Washington University [25]. CRISPR gRNAs for in vitro testing were identified using CRISPOR (crispor.tefor.net/) and synthesized as gBlocks (Integrated DNA Technologies, IDT) with…

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Bioinformatics Analyst Jobs in Mettawa IL \ Data Sciences Job Recruiters

The Genomic Research Center Computational Oncology group (GRC-CO) at  is seeking a highly motivated computational biologist/bioinformatics scientist to play an integral role in a multi-disciplinary team focused on developing new therapies for the treatment of cancer.  GRC is a center of excellence for bioinformatics, functional genomics, human genetics, and genomic…

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r – y-axis breaks with ggplot2 for a manhattan plot

I have a manhattan plot of genetic information: It was generated using the qqman package cran.r-project.org/web/packages/qqman/vignettes/qqman.html) in R which takes a dataframe of P-values, chromosome position and a gene position (for any biologists reading, this is a per gene manhattan hence the sparsity of signal). The data looks like this…

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RStudio | Information Technologies & Services

While running RStudio on your own computer is always an option, some projects or applications require collaborative work, high-power computing resources, or the ability to publish a dashboard or web application that others can view. ITS can support these uses through RStudio Team, a centrally-hosted service that allows users to…

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Elevated alpha diversity in disturbed sites obscures regional decline and homogenization of amphibian taxonomic, functional and phylogenetic diversity

Butchart, S. H. M. et al. Global biodiversity: Indicators of recent declines. Science 328, 1164–1168 (2010). ADS  CAS  Google Scholar  McGill, B. J., Dornelas, M., Gotelli, N. J. & Magurran, A. E. Fifteen forms of biodiversity trend in the Anthropogene. Trends Ecol. Evol. 30, 104–113 (2015). Google Scholar  Bradshaw, C….

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Seqlengths of x contains NA values!

Hello, I would like to use ORFik to determine the coverage of the different ORFs across the maize genome. I have ribo-seq data, the latest annotation file (a GFF3), and the v5 genome fasta file for B73. After running my code, three Large CompressedGRangesLists are created and none of them…

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What should I do with the fastq files of negative controls? – General Discussion

I am using QIIME2 and R packages for microbiome analysis.I think QIIME2 is the best tool, especially for researchers who are about to begin the microbiome analysis. My question is about the decontamination process. I have the fastq files of 16s microbiome sequences from skin tissue samples. The sequence files…

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GenScript is increasing its capacity for producing cGMP sgRNA and non-viral DNA payloads in order to keep project wait times to a minimum.

Dr. Ray Chen of GenScript in interaction with BioPharma APAC, reveals an aim to help accelerate the development of these therapies from research to clinic by providing high-quality cGMP sgRNA, Cas9 nuclease, and non-viral DNA payloads (ssDNA/dsDNA/circular minimized dsDNA) with fast turnaround time How is GenScript planning to meet the…

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Bioinformatics Data Scientist | Apex Systems

Job#: 1326086 Job Description: Bioinformatics Data Scientist 1326086 Location: Watertown, MA (Hybrid)Science/ Focus: Immunology – Cell TherapyTherapeutic Area(s): Immunology Job Overview: Our client is seeking a talented Bioinformatics Data Scientist to join their growing team and play a crucial role in the expansion of their platform. In this role, you will…

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Issue with VCF format while using Pharmcat

Hello everybody, I am using pharmcat tool’s prerprocessor feature to preprocessmy vcf file using the command > python3 pharmcat_vcf_preprocessor.py -vcf sample.vcf But I think there is some issue with my vcf file as this command outputs an error > Reading samples from sample.vcf … Saving output to . > >…

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Bioinformatics Analyst Position In North Chicago, IL

Job Description Job Title: Bioinformatic Analyst III The Genomic Research Center Computational Oncology group (GRC-CO) at Company is seeking a highly motivated computational biologist/bioinformatics scientist to play an integral role in a multi-disciplinary team focused on developing new therapies for the treatment of cancer. Company’s GRC is a center of…

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Nigerian researchers handover COVID-19 DNA vaccine candidate for preclinical trials

By JOHN ONAH, Abuja – Nigerian researchers engaged in the Tertiary Education Trust Fund-sponsored Vaccine Development Mega Research Project at Usman Danfodio University, Sokoto, have successfully handed over the Covid-19 DNA vaccine candidate for preclinical trials in Nigeria. The academics, in a symbolic handover of the vaccine candidate in Sokoto…

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Bioinformatics Research Scientist Job in Pennsylvania

UPCI Basic Research Administration – Pennsylvania-Pittsburgh – (23000703) A Bioinformatics Research Scientist position is available in the laboratory of Dr. Yu-Chiao Chiu at the UPMC Hillman Cancer Center at the University of Pittsburgh School of Medicine. We are seeking a highly motivated candidate with strong computational skills in…

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Post-doctoral Fellow in the Department of Medicine job with THE UNIVERSITY OF HONG KONG

Work type: Full-time Department: Department of Medicine, School of Clinical Medicine (20600) Categories: Senior Research Staff & Post-doctoral Fellow Applications are invited for appointment as Post-doctoral Fellow in the Department of Medicine, School of Clinical Medicine (Ref.: 519106), to commence as soon as possible for two years, with the possibility of renewal subject to satisfactory performance….

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Error while using rpy2

Hello everyone, I am trying to do some data analysis which requires both Python and R code chunks. So I am using R in Python using rpy2. Till now, the analysis worked fine, but when I tried doing the Differential Gene expression code, it gave me this error: RParsingError: Parsing…

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R/Bioconductor for Mass Spectrometry and Proteomics

News:Course – R/Bioconductor for Mass Spectrometry and Proteomics 0 Course: R/Bioconductor for Mass Spectrometry and Proteomics Format: Online, 27-29 March 2023 Overview This course will introduce participants to the analysis and exploration of mass spectrometry (MS) based proteomics data using R and Bioconductor. The course will cover all levels of…

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Solved source | Chegg.com

Transcribed image text: source (“www.openintro.org/stat/data/present.R&#8221😉 The data are stored in a data frame called present. 1. What years are included in this data set? What are the dimensions of the data frame and what are the variable or column names? 2. How do these counts compare to Arbuthnot’s? Are they…

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Research Fellow, Bioinformatician (Cancer Science Institute of Singapore) job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The position of Postdoctoral Fellow (PDF) — with an emphasis on computational cancer genomics — is immediately available at The Cancer Science Institute of Singapore (a part of The National University of Singapore). The postholder will work with the laboratories of Prof. Ashok Venkitaraman, on a project studying the…

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Solved Answer the following using RStudio code: A battery

Answer the following using RStudio code: A battery pack company knows that on purchase the battery life of a pair of their battery packs are normally distributed with an average life of 14 hours and a standard deviation of 1.25 hour. (a) The company would like to offer a money…

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Microbially produced vitamin B12 contributes to the lipid-lowering effect of silymarin

Animals As female mice/rats resist to HFD-induced obesity and NAFLD, male mice/rats were used to induce obesity and NAFLD model by HFD50. Male Wistar (~180 g body weight; 8 weeks old) rats were purchased from Shandong Laboratory Animal Center with the permission number of SCXK 2014–0007 and raised under thermoneutral housing…

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Research Initiatives Open up New Lucrative Horizons for the Liquid Biopsy Market, says Market.us

A liquid biopsy can be used as an alternative to conventional screening and surgical biopsies. This technology helps in the early detection of cancer cells. It also helps to prevent the disease from reaching a stage that could negatively impact the patient’s survival. The liquid biopsies are blood-based and extremely…

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Updating the Orphan Drug Act for the next 40 years

This month marks the 40th anniversary of the Orphan Drug Act. Since it was signed into law in 1983, the FDA has approved more than 1,100 treatments for rare diseases. The act also created an industry that didn’t exist in the United States before its enactment, enabling the formation of…

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Improving convergence for bulk Iron (bcc Fe)

Dear CP2K users, I’m struggling with convergence for bulk Fe, i.e. 3x3x3 supercell containing 54 Fe atoms. I wanted to simulate adsorption of different organic molecules on Fe(100) slab later, so this is my starting point. During GEO_OPT or CELL_OPT runs I sporadically encounter SCF issues like this: …    33 Broy./Diag….

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fail to open index BAM file”

Dear all, I applied CNVkit to call copy number variations in a case-control study, with vascular malformation samples as case and healthy individuals as control using the following command. /ifs9/B2C_RD_P5/lijia3/CONDA/bin/python /ifs9/B2C_RD_P5/lijia3/CNVkit/cnvkit/cnvkit.py batch /zfsyt1/B2C_RD_P5/lijia3/VM/*.bam –normal /zfsyt1/B2C_RD_P5/lijia3/VM_controls/Control/Control-Kid/*.bam –targets BGI_Exome_V4_kit_200bp.bed –antitargets my_antitargets.bed –annotate refFlat.txt –fasta /ifs7/B2C_SGD/PROJECT/PP12_Project/analysis_pipeline/HPC_chip/db/aln_db/hg19/hg19_chM_male_mask.fa –access access.ucsc.hg19.bed –output-reference VM_normal_adult_reference.cnn –output-dir results_Kid/ –diagram…

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Another Black Screen Problem – RStudio IDE

A few days ago, I had a black screen when I tried to open RStudio. RStudio is a black screen that won’t close – #2 by andresrcs I took the advice given in the above link and made the change. However, I still have a problem, I was eventually able…

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Create array of for loop results – General

Hello, I’m loading 20 files into R using the below script (they’re matrices of 500 x 500). I would like create an array of all the loaded files. is there a way I can have R do it automatically? ##Read files names filenames <- list.files(path=”/Users/dana……..”) ###Load all files for(i in…

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Gini coefficient TCR repertoire

Gini coefficient TCR repertoire 1 Hi, I would like to calculate the Gini coefficient for my TCR repertoire data. I have seen that this can be calculated using the DescTools and ineq packages in R, however from the package documentation, I am unclear what input is required in the context…

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Sr. Scientist, Heme BioInformatics, Translational Medicine Onc R&D – AstraZeneca

AstraZeneca is a global, science-driven biopharmaceutical company. We are dedicated to discovering, developing, and delivering innovative, meaningful medicines and healthcare solutions that enrich the lives of patients. The vision of AstraZeneca Oncology is to redefine cancer, redefine our solutions to cancer, and restore patients’ lives. Within Hematology R&D, we are…

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Bioinformatics Analyst (Remote) – Rangam Consultants Inc.

Job Title: Bioinformatics Analyst Length of the assignment: 6 mo – 12 months This is a remote position. PhD or Masters preferred. The client is seeking a highly motivated computational biologist/bioinformatics scientist to play an integral role in a multi-disciplinary team focused on developing new therapies for the treatment of…

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getTable ignores query ranges

HI everyone. I have a set of mouse SNPs (~974) from GRCm39 that I’m trying to get either GERP or UCSC Conservation scores on. To do this, I’m using rtracklayer to try to query the ranges of the SNP and return the multiz35way conservation score. However, when I do this,…

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Definition of sequencing in Microbiology, Biology.

Examples of sequencing in the following topics: Sequences A sequence is an ordered list of objects (or events). Also, the sequence $(1, 1, 2, 3, 5, 8)$, which contains the number $1$ at two different positions, is a valid sequence. Sequences can be finite, as in this example, or infinite,…

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r – Changing the data frame of a ggplot graph from a dropdown menu in Shiny

I am trying to change the data frame that ggplot uses to render a graph given a selection of a drop down menu. The dropdown menu works but the graph will not render. for reference ‘school’ is a set of strings with the names of teams. library(shiny) library(shinydashboard) library(ggplot2) ui…

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a problem with getBM

I want to add gene name information to my expression file, I use Biomart for this, but actually i did not get any result from getBM, my codes in R: upregul<-read.csv(file.choose()) View(upregul) library(biomaRt) listEnsembl() ensembl <- useEnsembl(biomart = “genes”) ensembl_ids<-(upregul) View(ensembl_ids) datasets <- listDatasets(ensembl) head(datasets) ensembl_con<-useEnsembl(“ensembl”,dataset=”hsapiens_gene_ensembl” ) attr<-listAttributes(ensembl_con) filters<-listFilters(ensembl_con) theBm<-getBM(attributes…

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r – wrapping the labels of legend in ggplot ZINB model

I need help in wrapping the labels of legend in ggplot. I tried various option including str_wrap(model, width=20) scale_colour_discrete(labels = function(x) str_wrap(x, width = 5)) guides(colour = guide_legend(nrow = 2)) but without any success library(ggplot2) ggplot(coefs, aes(x = estimate, y = term, colour = model)) + geom_vline(xintercept = 1, lty…

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EMDB < EMD-28585

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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How do I preview in R?

Other ways to preview the file • Select the file in the Files panel and click the Preview button, or. • Select the file in the Files panel and select Preview on the File menu. How do I show preview in R? You can preview your file by using the…

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Bioinformatics Scientist (PhD) (R Programming/Genomics Data Analysis) – Rangam Consultants Inc.

Location – Position is 50% on-site. Responsibilities Under the guidance of senior analysts, define and execute biomarker data analysis plan for late-stage oncology trials and other datasets Perform analysis of clinical and biomarker datasets (e.g., large-scale omics datasets including RNASeq, Exome and Whole Genome Sequencing, single cell sequencing) and derive…

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Long term culturing of CHO cells: phenotypic drift and quality attributes of the expressed monoclonal antibody

Bailey LA, Hatton D, Field R, Dickson AJ (2012) Determination of Chinese hamster ovary cell line stability and recombinant antibody expression during long-term culture. Biotechnol Bioeng 109:2093–2103 CAS  Google Scholar  Barbosa MD (2011) Immunogenicity of biotherapeutics in the context of developing biosimilars and biobetters. Drug Discov Today 16:345–353 CAS  Google…

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Isolation and characterisation of exosomes from Chinese hamster ovary (CHO) cells

Belliveau J, Papoutsakis ET (2022) Extracellular vesicles facilitate large-scale dynamic exchange of proteins and RNA among cultured Chinese hamster ovary and human cells. Biotechnol Bioeng 119(5):1222–1238. doi.org/10.1002/bit.28053 Article  CAS  Google Scholar  Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle…

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How to modify plot title in R using ggplot2

Here is how to add and modify the plot title in R using ggplot2 in many ways. After adding the ggplot2 title and subtitle, you might want to change the alignment, color, and size, add a bold effect to all or a few words, and do other customizations. Here are…

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r – Percentages in the wrong position in ggplot2

I’m trying to plot a graph for a likert test using ggplot2 and I would like to have the percentages values appearing on the graph. I’ve created a df with all the averages and percentages so I could write it on the graph. It all seems to be working good,…

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Bioconductor – MEDIPS

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see MEDIPS. DNA IP-seq data analysis Bioconductor version: 3.2 MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of…

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Magrolimab Plus Rituximab/Chemo Elicits Deep Responses in Relapsed/Refractory DLBCL

The combination of magrolimab, rituximab (Rituxan), gemcitabine, and oxaliplatin produced deep, durable responses in patients with relapsed or refractory diffuse large B-cell lymphoma (DLBCL), according to preliminary results from a cohort of a phase 1b trial (NCT02953509) presented at the 2022 ASH Annual Meeting. At a median follow-up of 11.3…

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Bioconductor – hgu95bcdf

DOI: 10.18129/B9.bioc.hgu95bcdf     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see hgu95bcdf. hgu95bcdf Bioconductor version: 3.10 A package containing an environment representing the HG_U95B.CDF file. Author: The Bioconductor Project Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“hgu95bcdf”)):…

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Transcription factor EB regulates phosphatidylinositol-3-phosphate levels that control lysosome positioning in the bladder cancer model

Cell culture and treatments Bladder cancer cells lines RT4, MGHU3, RT112, KU19-19, JMSU1, T24 and TCCSup were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA, USA), supplemented with 10% Fetal Bovine Serum (FBS; Eurobio, Courtaboeuf, France). Normal human urothelium (NHU) cells were from Jennifer Southgate (University of York, UK). NHU were…

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PolaR-ICE Effective as Second-line Treatment in DLBCL, Bridge to Autologous Stem Cell Transplant

Adding polatuzumab vedotin (polatu-zumab, Polivy) to rituximab-based salvage therapy produced strong responses and allowed 61% of patients who had failed their first treatment for diffuse large B-cell lymphomas (DLBCL) to successfully bridge to autologous stem cell transplant (ASCT), according to a phase 2 study (NCT04665765).1 Results from 41 patients, presented…

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Sharing GWAS summary statistics results in more citations

Analyses The GWAS Catalog10 is an established and high-quality repository of curated human GWAS results, providing easy access to summary statistics made public by authors (via curator inclusion or author submission). Its large coverage (400,000+ associations from 5690 publications as of May 2022) and its easy-to-access statistics make it an…

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First detection of Ixodiphagus hookeri (Hymenoptera: Encyrtidae) in Ixodes ricinus ticks (Acari: Ixodidae) from multiple locations in Hungary

Chala, B. & Hamde, F. Emerging and re-emerging vector-borne infectious diseases and the challenges for control: A review. Front. Public Health doi.org/10.3389/fpubh.2021.715759 (2021). Article  Google Scholar  Jongejan, F. & Uilenberg, G. The global importance of ticks. Parasitology 129, S3–S14 (2004). Google Scholar  Hornok, S., Kováts, D., Horváth, G., Kontschán, J….

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Bioinformatics Scientist (Statistical Programming/Data Manipulation) – Rangam Consultants Inc.

Hybrid role Research Scientist, Early Development Predictive Sciences We are seeking an innovative scientist to join our Informatics Predictive Sciences team. Roles and responsibilities: Performing computational biology analysis for exploration and interpretation of omic datasets, including bulk and single-cell RNASeq, DNA methylation, Exome/Genome sequencing, cytokine, and proteomic data. Integrative analysis…

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Molecular epidemiology of CRKP | IDR

Introduction Klebsiella pneumoniae (Kp; K. pneumoniae) is an important hospital and community-acquired pathogen that primarily causes pneumonia, urinary tract infections, bloodstream-associated infections, meningitis, and pyogenic liver abscess.1–3 Carbapenem antibiotics represent the most important treatment for Enterobacteriaceae; however, with the widespread use of such antibiotics, carbapenem-resistant K. pneumoniae (CRKP) is increasingly…

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R ggplot2: Bar chart for the answers on the question with multiple response option

I want to make a bar chart for the answers on the question with multiple response option. The code works but the graph shows additional column without the title. Where does this column come from and how can I remove it? Is it somehow related to NA? This is the…

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Maternal diet induces persistent DNA methylation changes in the muscle of beef calves

Gicquel, C., El-Osta, A. & Le Bouc, Y. Epigenetic regulation and fetal programming. Best Pract. Res. Clin. Endocrinol. Metab. 22, 1–16 (2008). CAS  Google Scholar  Godfrey, K. M. & Barker, D. J. Fetal programming and adult health. Public Health Nutr. 4, 611–624 (2001). CAS  Google Scholar  Encinias, H. B., Lardy,…

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Solved Data analysis with RStudio Consider the Sacramento

Data analysis with RStudio Consider the Sacramento real estate data file (Sacramentorealestatetransactions.csv) attached to this exercise. Create a R script with Rstudio to: 1. Display the structure and content of the file using the function head(). 2. Display the descriptive statistics of the data contained in the file. 3. Clean…

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Neither R nor RStudio will execute any plot

This issue suddenly happened without any obvious reason. R nor RStudio will execute any type of plot be it ggplot or a simple hist(). Nothing comes up in the plot viewer window and the console continually runs the code until I hit stop and the applications crash. This happens in…

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How to translate CDS to an amino acid sequence

How to translate CDS to an amino acid sequence 2 How to translate CDS to amino acid sequence? This site shows CDS and translations but no explanation on how to get there. translation CDS sequencing • 1.3k views • link updated 2 hours ago by vvasta • 0 • written…

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Bioinformatics Analyst – Virology – J. Craig Venter Institute

JCVI – La Jolla, CA Job Responsibilities: The Bioinformatics Analyst – Virology will work as a member of the Scheuermann bioinformatics research team on analysis of viral genomic, immune epitope, protein structure, and related data for the purpose of vaccine development for newly emerging viral pathogens as part of a…

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Principal/Associate Director Pre-clinical Bioinformatics – Repare Therapeutics

Repare Therapeutics provides equal employment opportunities to all employees and applicants for employment and prohibits discrimination and harassment of any type without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal,…

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unable to open file or unable to determine types for file bed file

Error: unable to open file or unable to determine types for file bed file 3 I’m trying to do a bedtools compare on a couple of bed files. One of the bed files keeps throwing this error: Error: unable to open file or unable to determine types for file My…

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email – Troubleshooting slurm e-mail settings

I am trying to setup a slurm installation and I have advanced towards the e-mail stage. So far I do not receive any mails. I have a working setup using msmtp-mta and msmtp. When I batch a script the slurmctld log shows email msg to **@**: Slurm Job_id=73 Name=example_script.sh Began,…

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A chromosome-level genome assembly of Plantago ovata

Genome assembly and chromosome identification A Plantago ovata genome reference was generated by utilizing a total of 5.98 M (7 cells, 40.21 Gb, N50 = 10.45 Kb, 50 bp–121.17 Kb) PacBio long reads and 636.5 million (47.74 Gb) Hi-C short-reads. PacBio reads were used to assemble contigs, while Hi-C reads were used to achieve chromosome-level assembly. The final…

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sagemath package currently absent from bookworm

Successfully built Sagemath 9.6 on Bookworm (“apt dist-upgrade”-ed as of 25 January 2023) using the following script. (It seems to have partially built 9.7, and that build might be fixable by an interested someone.) The important piece seems to be ./configure –without-system-gcc –without-system-pari –without-system-singular to avoid the version conflicts reported…

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Fluorescent aptasensor based on the MNPs-CRISPR/Cas12a-TdT for the determination of nasopharyngeal carcinoma-derived exosomes

doi: 10.1007/s00604-023-05657-7. Affiliations Expand Affiliations 1 Department of Radiotherapy, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China. 2 Department of Pharmacy, Zigong Third People’s Hospital, Zigong, 643020, Sichuan, China. 3 Department of Otorhinolaryngology Head and Neck Surgery, Shenzhen Fuyong People’s Hospital, Shenzhen,…

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Critical criteria for filtering variants by VariantFiltration

Critical criteria for filtering variants by VariantFiltration 0 Hi all. I run the GATK VariantFiltration with the following parameters (according to GATK recommendation) to find robust variants. Then I used them as input for annotating variants. Do you have any suggestions for better filtration? Is it recommended to run VariantFiltration…

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WSM Williams-Sonoma Inc. Common Stock (DE)

Outlook: Williams-Sonoma Inc. Common Stock (DE) is assigned short-term Ba1 & long-term Ba1 estimated rating.Dominant Strategy : BuyTime series to forecast n: 27 Jan 2023 for (n+16 weeks)Methodology : Reinforcement Machine Learning (ML) Abstract Williams-Sonoma Inc. Common Stock (DE) prediction model is evaluated with Reinforcement Machine Learning (ML) and Wilcoxon…

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Artificial Intelligence in Genomics Market Industry Analysis –

The Global Artificial Intelligence in Genomics Market size accounted for USD 471 Million in 2021 and is estimated to reach USD 18,213 Million by 2030. Artificial Intelligence in Genomics Market Dynamics The rapid expansion of genomics research data sets, the emergence of startups in the sector, and significant research and…

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r – Significance comparison in ggplot not working with verbatim identical annotation entries

I want to plot significance differences using ggsignif::geom_signif() but run into issues if the significance description is identical for multiple comparisons. Consider the following toy data set: structure(list(x = c(“a1”, “a2”, “b3”, “b4”, “c5”, “c6”), treat = c(0, 1, 0, 1, 0, 1), group = c(“a”, “a”, “b”, “b”, “c”,…

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Species richness of bat flies and their associations with host bats in a subtropical East Asian region | Parasites & Vectors

Scott M, Dobson A. The role of parasites in regulating host abundance. Parasitol Today. 1989;5:176–83. CAS  Google Scholar  Tompkins D, Dobson A, Arneberg P, Begon M, Cattadori I, Greenman J, et al. Parasites and host population dynamics. The ecology of wildlife diseases. 2002; 45–62. Thomas F, Poulin R, Brodeur J….

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Bioconductor – RTCGA.clinical

DOI: 10.18129/B9.bioc.RTCGA.clinical     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see RTCGA.clinical. Clinical datasets from The Cancer Genome Atlas Project Bioconductor version: 3.8 Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from gdac.broadinstitute.org/. Clinical data format…

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\( \begin{aligned} 8: 52 & \text { will } \\ 4 \text

Transcribed image text: 8:524 Safari ​ will 80​ Step 1/4 Done a) To produce a histogram of the Dodgers salary data in R, you can use the following code: 1 Iibrary (ggplot2) 2 dodgers salary <- c(19000, 15730, 15217, 14727,10000,9517,9250,9000,8000,7500 ) 3 ggplot(data – data.frame(dodgers_salary), aes(x = dodgers_salary)) + 4 geom_histogram(fil1 ” “blue”, binwidth=…

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Bioconductor – GMRP

DOI: 10.18129/B9.bioc.GMRP     GWAS-based Mendelian Randomization and Path Analyses Bioconductor version: Release (3.11) Perform Mendelian randomization analysis of multiple SNPs to determine risk factors causing disease of study and to exclude confounding variabels and perform path analysis to construct path of risk factors to the disease. Author: Yuan-De Tan…

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CTCF: an R/bioconductor data package of human and mouse CTCF binding sites

. 2022 Dec 16;2(1):vbac097. doi: 10.1093/bioadv/vbac097. eCollection 2022. Affiliations Expand Affiliations 1 Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA. 2 Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA. 3 Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA. 4 Curriculum in…

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New Technology Developments in CRISPR and CAS Gene Market to Grow

CRISPR and CAS Gene Market The CRISPR and CAS Gene Market Report Overview 2022 Qualitative Research Study accomplished by Stratagem Market Insights research’s database of 350 pages, titled “Global CRISPR and CAS Gene Market Study” with 100+ market data Tables, Pie Charts, Graphs & Figures spread through Pages and easy-to-understand…

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Alternatives to perform peptide identification in Bioconductor version ‘3.16’?

Alternatives to perform peptide identification in Bioconductor version ‘3.16’? 0 @23d16096 Last seen 4 hours ago United States MSGFplus and rTANDEM are both deprecated in Bioconductor version ‘3.16’. Are there any alternatives to perform peptide identification with spectral libraries? Code should be placed in three backticks as shown below #…

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Research Fellow, Bioinformatician, Cancer Science Institute job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The position of Postdoctoral Fellow (PDF) in computational cancer genomics is immediately available at The Cancer Science Institute of Singapore (The National University of Singapore). This PDF will lead a newly funded project in the laboratory of Dr. Jason Pitt that will explore how germline genetics and cell-of-origin…

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Chemotherapy in the afternoon proved to be effective for female lymphoma patients

Chemotherapy is a commonly used regimen for cancer treatment, but it is also a double-edged sword. While the drugs are highly effective at killing cancer cells, they are also notorious for killing healthy cells in the body. As such, minimizing the drug’s damage to the patient’s body is necessary for…

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The Global Bioinformatics Market size is expected to reach $19.9 billion by 2028, rising at a market growth of 12.5% CAGR during the forecast period

ReportLinker In order to serve several fields of scientific study, including biomedicine, bioinformatics—a mix of biology and information technology—links biological data with methods for information storage, dissemination, and analysis. New York, Jan. 27, 2023 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “Global Bioinformatics Market Size, Share &…

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bioinformatics – How do I download a large number of GenBank sequences using entrez_fetch in R?

I am trying to download sequence data from 1283 records in GenBank using rentrez. I’m using the following code, first to search for records fitting my criteria, then linking across databases, and finally fetching the sequence data: # Search for sequence ids in biosample database search <- entrez_search(db = “biosample”,…

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For Loop to move grobs in ggplot using editGrob only working for last element in R

Based on this question: Customize label element position in ggplot using gtable/grob The answer by stackoverflow.com/users/5193830/valentin-%c8%98tefan was fantastic and I learnt a lot from it. However I would like to apply editGrob to more than one gPaths at a time. Code: #Dependencies require(ggplot2); require(grid); require(png); require(RCurl) ; require(dplyr) #Data Wrangling…

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r – Continuous changing linewidth becomes transparent in ggplot

I am experimenting with the linewidth aesthetic in ggplot and mainly how to use it for continuously changing a line. When I am trying to create a continuously growing linewidth line, it becomes transparent. Here is some reproducible code: library(ggplot2) x = seq(0,2*pi,length.out=10000) y = sin(x) df<-data.frame(x=x,y=y, width = seq(from…

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Postdoctoral Scholar – Plant Bioinformatics in Houghton, MI for Michigan Technological University

Details Posted: 27-Jan-23 Location: Houghton, Michigan Salary: Open Department: College Forest Resources & Envr Sci Sub Department: To perform this job successfully, an individual must be able to perform each essential duty satisfactorily. The requirements listed below are representative of the knowledge, skill, and/or ability required. Reasonable accommodations may be…

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[8.15 MB] Download Free of Importing a .csv file to R Studio using the read.csv function Mp3 (05:56 Min)

Importing a .csv file to R Studio using the read.csv function (8.15 MB) – Free Download Importing a .csv file to R Studio using the read.csv function (05:56 Min) mp3 – Download lagu mp3 Importing a .csv file to R Studio using the read.csv function on MP3 Juice. Title Importing…

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Learn how to use R and RStudio for research | E-News

Hosted by WVU Libraries, this series includes two special workshops on applying the knowledge you have acquired to perform special functions. First Steps with R and RStudioThis workshop will introduce participants to using R and RStudio. No prior programming knowledge is required, just a basic understanding of computer files and…

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Allergy Diagnostics Market Size & Share to Surpass $8873.68

WASHINGTON, Jan. 27, 2023 (GLOBE NEWSWIRE) — Vantage Market Research analyses that the Allergy Diagnostics Market which was $ 4821.90 Million in 2021, would rocket up to $ 8873.68 Million by 2028, and is expected to undergo a CAGR of 10.70% during the forecast period 2022 to 2028. Vantage Market…

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Mutations in the database don’t appear in the portal

cBioportal: Mutations in the database don’t appear in the portal 0 Hi! I am working with the invasive breast cancer database from the pancancer project of TCGA downloaded through cbioportal (www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018). Working with it in R, I found a mutation in HINT3 (Tumor Sample Barcode TCGA-A8-A09A-01), but when I wanted…

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r – Error in GenomeInfoDb library while trying to use Biostrings

I’m trying to use the library Biostring for some fasta files analysis of virus, when I try to use the package the console displays an error: library(Biostring) # your input # ————–console output Loading required package: GenomeInfoDb Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(j <- i[[1L]], c(lib.loc,…

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EMDB < EMD-13594

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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