Tag: R

Accepted r-bioc-rgsepd 1.28.0-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 17 May 2022 08:43:38 +0200 Source: r-bioc-rgsepd Architecture: source Version: 1.28.0-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-rgsepd (1.28.0-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1:…

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Accepted r-bioc-scrnaseq 2.10.0+ds-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 17 May 2022 07:49:00 +0200 Source: r-bioc-scrnaseq Architecture: source Version: 2.10.0+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-scrnaseq (2.10.0+ds-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version:…

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Variant #0000255165 (NC_000010.10:g.123278248A>G, FGFR2(NM_000141.4):c.939+1245T>C) – Global Variome shared LOVD

Variant #0000255165 (NC_000010.10:g.123278248A>G, FGFR2(NM_000141.4):c.939+1245T>C) Chromosome 10 Allele Unknown Affects function (as reported) Probably does not affect function Affects function (by curator) Not classified Classification method – Clinical classification likely benign DNA change (genomic) (Relative to hg19 / GRCh37) g.123278248A>G DNA change (hg38) g.121518734A>G Published as FGFR2(NM_022970.3):c.1035T>C (p.Y345=) ISCN – DB-ID FGFR2_000119 Variant remarks VKGL data sharing initiative Nederland Reference – ClinVar ID – dbSNP ID – Origin CLASSIFICATION record Segregation –…

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Parse a file of strings in python separated by newline into a json array

I don’t see where you’re actually reading from the file in the first place. You have to actually read your path_text.txt before you can format it correctly right? with open(‘path_text.txt’,’r’,encoding=’utf-8′) as myfile: content = myfiel.read().splitlines() Which will give you [‘/gp/oi/eu/gatk/inputs/NA12878_24RG_med.hg38.bam’, ‘/gp/oi/eu/gatk/inputs/NA12878_24RG_small.hg38.bam’] in content. Now if you want to write this…

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Single-cell eQTL models reveal dynamic T cell state dependence of disease loci – Nature – Alert Breaking News

Wei, K. et al. Notch signalling drives synovial fibroblast identity and arthritis pathology. Nature 582, 259–264 (2020). ADS CAS PubMed PubMed Central Article Google Scholar  Cembrowski, M. S. & Menon, V. Continuous variation within cell types of the nervous system. Trends Neurosci. 41, 337–348 (2018). CAS PubMed Article Google Scholar  Maurano, M. T. et al. Systematic localization of…

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genetic epidemiology postdoc

Qualification Details. Objective/methods: This report investigates by histology, immunohistochemistry and in situ hybridization the histological and . Philip Lupo, Ph.D. Dr. Lupo is a co-principal investigator in the Systems Epidemiology of Cancer Training Program and an associate professor in the Section of Hematology-Oncology in the Department of Pediatrics. . «Genetic…

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Unicode Characters in ggplot2 PDF Output

As Ben suggested, cairo_pdf() is your friend. It also allows you to embed non-postscript fonts (i.e. TTF/OTF) in the PDF via the family argument (crucial if you don’t happen to have any postscript fonts that contain the glyphs you want to use). For example: library(ggplot2) cairo_pdf(“example.pdf”, family=”DejaVu Sans”) qplot(Sepal.Length, Petal.Length,…

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Open API Market Size, Trends and Forecast to 2029

New Jersey, United States – The Open API Market report includes the upcoming challenges and opportunities in the market. It ensures a strengthened position in the market and a growing product portfolio by providing all the important details related to the market growth. It reveals some of the key insights and focuses…

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Oncolytic Adenovirus with SPAG9 shRNA Driven by DD3 Promoter Improved the Efficacy of Docetaxil for Prostate Cancer

. 2022 Apr 30;2022:7918067. doi: 10.1155/2022/7918067. eCollection 2022. Affiliations Expand Affiliations 1 Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu Province, China. 2 Department of Urology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China. Free PMC article Item in Clipboard Meng…

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Accepted r-bioc-rsubread 2.10.0-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 12 May 2022 14:00:29 +0200 Source: r-bioc-rsubread Architecture: source Version: 2.10.0-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-rsubread (2.10.0-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version:…

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Genetic and chemotherapeutic influences on germline hypermutation

DNM filtering in 100,000 Genomes Project We analysed DNMs called in 13,949 parent–offspring trios from 12,609 families from the rare disease programme of the 100,000 Genomes Project. The rare disease cohort includes individuals with a wide array of diseases, including neurodevelopmental disorders, cardiovascular disorders, renal and urinary tract disorders, ophthalmological…

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RPostgreSQL connections are expired as soon as they are initiated with doParallel clusterEvalQ

I was able to reproduce your problem locally. I am not entirely sure but I think the problem is related to the way clusterEvalQ works internally. For example, you say that dbGetQuery(con, “select inet_client_port()) gave you the client port output. If the query was actually evaluated/executed on the cluster nodes…

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COVID-19 vaccines in liver transplant recipients

Introduction Three waves of world wild emerging severe infectious disease pandemics have been presented during this century because of the coronavirus. The severe acute respiratory syndrome (SARS) outbreak in southern China since 2002 has spread to 8096 cases from 29 countries, with a mortality of 9.6%.1 Middle East respiratory syndrome…

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Cogent Biosciences Reports Recent Business Highlights and First Quarter 2022 Financial Results

Cogent Biosciences, Inc. Initial bezuclastinib APEX data to be presented at the European Hematology Association (EHA) 2022 Annual Congress Building a portfolio of discovery stage programs, creating potential best-in-class small molecule kinase inhibitors for genetically defined oncology indications and rare diseases Ended 1Q 2022 with $191.0 million in cash, sufficient…

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CALITHERA BIOSCIENCES, INC. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS (form 10-Q)

You should read the following discussion and analysis of our financial condition and results of operations in conjunction with our unaudited condensed consolidated financial statements and related notes included in Part I, Item 1 of this report. This Quarterly Report on Form 10-Q contains forward-looking statements within the meaning of…

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Error while installing “object I is not exported by namespace:S4Vectors

met a problem while installing the LTLA/SingleR 1.5.3, urgent, thank you very much for help installing to /home/binf0xx/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-SingleR/00new/SingleR/libs ** R ** inst ** byte-compile and prepare package for lazy loading Error: object ‘I’ is not exported by ‘namespace:S4Vectors’ Execution halted ERROR: lazy loading failed for package ‘SingleR’ removing ‘/home/binf0xx/R/x86_64-pc-linux-gnu-library/4.0/SingleR’ Read…

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Z697 – YFull YTree Info

R-Z697 – YFull YTree Info SNPs currently defining R-Z697 Z697     Sample ID Country / Language Info Ref File Testing company Statistics Status YF009397 Sweden (Västra Götalands län) R-Z697* —— Hg19 .BAM FTDNA (Y500) 81X, 14.4 Mbp, 165 bp YF084333 Italy (Chieti) R-FT285492 —— Hg38 .BAM Dante Labs 14X, 23.4…

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Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data

Introduction Incipient species are critical for evolutionary biologists to study speciation, but they also challenge taxonomy due to gene flow or ancestral polymorphism. The former and contrasting population size lead to larger intraspecific than interspecific variations, a phenomenon called the species-definition anomaly zone (Jiao and Yang, 2021). The latter results…

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Bioconductor – htrat230pmprobe

DOI: 10.18129/B9.bioc.htrat230pmprobe     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see htrat230pmprobe. Probe sequence data for microarrays of type htrat230pm Bioconductor version: 3.14 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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First notebook – looking for advice : kaggle

Hello r/kaggle This is my first post here and I am pretty new to kaggle too. I am an engineer with some experience in data analytics but completely new to machine learning. I want to get into this world to bring my skills and my career to the next level….

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R: MA-Plot

R: MA-Plot plotMA {limma} R Documentation MA-Plot Description Creates an MA-plot with color coding for control spots. Usage plotMA(MA, array=1, xlab=”A”, ylab=”M”, main=colnames(MA)[array], xlim=NULL, ylim=NULL, status, values, pch, col, cex, legend=TRUE, zero.weights=FALSE, …) Arguments MA an RGList, MAList or MArrayLM object, or any list with components M containing log-ratios and…

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Senior Research Associate, Bioinformatics at Kite Pharma

Job details Job type full-time Full job description Job description At kite pharma we are revolutionizing the treatment for cancers through immunotherapy through novel breakthrough technologyWe have developed and launched best in class car-t therapy yescarta, currently curing patients from previously intractable b-cell malignanciesWe are using our expertise to apply…

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Associate Bioinformatics Scientist at Flagship Pioneering, Inc.

Company Summary: Who Are We? Founded by Flagship Pioneering, Empress pioneers the future of small molecule drugs through the discovery of pharmacologic loci. The company’s product platform leverages AI and multi’omic data from thousands of humans around the globe to discover novel, important small molecules inside of humans and their cognate mechanisms…

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Adjunct Professor Track Faculty Position – Bioinformatics job with University of California-Irvine

Founded in 1965, UC Irvine combines the strengths of a major research university with the bounty of an incomparable Southern California location. Over five remarkable decades, UCI has become internationally recognized for efforts that are improving lives through research and discovery, fostering excellence in scholarship and teaching, and engaging and…

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Problem on R when creating a PCA plot

Problem on R when creating a PCA plot 0 A very weird thing is happening to me on R, the first time i installed “ggfortify” pacakage to create a PCA plot, the result was an Rplots.pdf file, it worked perfectly. The second time i used it, with the same exact…

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A*STAR – Agency for Science, Technology and Research hiring Bioinformatics Specialis, Laboratory of Systems Biology & Data Analytics, GIS in Singapore, Singapore

 The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to achieve extraordinary improvements in human health and public prosperity. GIS is dedicated to creating a social culture that is…

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Help me understand the Nanopore fastqc results

Help me understand the Nanopore fastqc results 2 Hi, I have got my first Nanopore sequencing data and the first step was to see if the data is good. Has anyone has any experience with this kind of data and can tell me how to interpret the results. The whole…

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Detection of candidate gene LsACOS5 and development of InDel marker for male sterility by ddRAD-seq and resequencing analysis in lettuce

Ryder, E. J. Lettuce, Endive and Chicory (CABI Publishing, 1999). Google Scholar  Seki, K. et al. A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.). Hortic. Res. 7, 1–14 (2020). Article  Google Scholar  Odland,…

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Pacific Biosciences Makes Progress on Sequencer Development, Amends Invitae Deal

NEW YORK – Pacific Biosciences said on Wednesday that it has made progress on the development of two sequencing platforms and announced that it is amending payment terms for its collaboration with Invitae on a high-throughput whole-genome sequencer. The Invitae collaboration is one of three R&D projects PacBio officials mentioned…

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Recent questions tagged fasta – Q&A

Most popular tags python javascript html java css reactjs c# php r sql arrays pandas c++ android jquery DataFrame python-3.x node.js c mysql list flutter JSON ios typescript sql-server swift string angular regex laravel excel django dictionary dart bash numpy postgresql loops oracle vba linux angularjs function for-loop spring spring-boot…

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Visualizing Transcript Structure and Annotation using ‘ggplot2’ version 0.99.8 from GitHub

The goal of ggtranscript is the simplify the process of visualizing transcript structure and annotation. To achieve this, ggtranscript introduces 5 new geoms (geom_range(), geom_half_range(), geom_intron(), geom_junction() and geom_junction_label_repel()) as well as several helper functions. As a ‘ggplot2’ extension, ggtranscript inherits ‘ggplot2’s familiarity and flexibility, enabling users to intuitively adjust…

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[Solved] tryCatch not catching error produced by install.packages within RStudio

RStudio does not exectute the normal install.packages but instead does its own thing: look at the code in RStudio: > install.packages function (…) .rs.callAs(name, hook, original, …) <environment: 0x3e4b478> > .rs.callAs function (name, f, …) { withCallingHandlers(tryCatch(f(…), error = function(e) { cat(“Error in “, name, ” : “, e$message, “\n”,…

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Recent developments in miRNA based recombinant protein expression in CHO

Aguiar TQ, Santos SB, Martins IM, Domingues L, Oliveira C (2019) Production and bioengineering of recombinant pharmaceuticals. Proteins: sustainable source, processing and applications. Elsevier, Amsterdam, pp 259–293 Chapter  Google Scholar  Amadi IM, Agrawal V, Christianson T, Bardliving C, Shamlou P, LeBowitz JH (2020) Inhibition of endogenous miR-23a/miR-377 in CHO cells…

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Landscape of helper and regulatory antitumour CD4+ T cells in melanoma

Sallusto, F. & Lanzavecchia, A. Heterogeneity of CD4+ memory T cells: functional modules for tailored immunity. Eur. J. Immunol. 39, 2076–2082 (2009). CAS  PubMed  Article  Google Scholar  Swain, S. L., McKinstry, K. K. & Strutt, T. M. Expanding roles for CD4+ T cells in immunity to viruses. Nat. Rev. Immunol….

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nf-core presentation – HackMD

<!– .slide: data-background=”raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg&#8221; –> <a href=”nf-co.re”><img src=”raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-darkbg.svg&#8221; width=”60%”></img></a> # What is nf-core\? [Maxime U Garcia](https://maxulysse.github.io/) ▸ [<i class=”fa fa-twitter” aria-hidden=”true”></i>@gau](https://twitter.com/gau/) | [<i class=”fa fa-github” aria-hidden=”true”></i>@maxulysse](https://github.com/maxulysse/) [Karolinska Institutet](https://ki.se/) | [Science for Life Laboratory](https://www.scilifelab.se/) Sweden — ## Overview – 🗄️ [Barntumörbanken](https://ki.se/forskning/barntumorbanken/) – 🧬 [NGI](https://ngisweden.scilifelab.se/) – 🍬 [Nextflow](https://www.nextflow.io/) – 🧙 [nf-core](https://nf-co.re/) — ##…

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[BioC] rtracklayer 1.6: invalid class “ucscCart” object

Dear Bioc, Following the rtracklayer documentation, section 2.2.4, ‘A Shortcut’, I encounter the following error browseGenome (subTargetTrack) Error in validObject(.Object) :invalid class “ucscCart” object: superclass “ANYTHING” not defined in the environment of the object’s class traceback () 13: stop(msg, ” “, errors, domain = NA)12: validObject(.Object)11: initialize(value, …)10: initialize(value, …)9:…

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scRNAseq analysis – h5ad file conversion to Seurat format

scRNAseq analysis – h5ad file conversion to Seurat format 0 Hi all. I have a single .h5ad file that contains scRNAseq data from several samples. I would like to convert it so that I can open it in Seurat (I am comfortable with R, but not with Python). I have…

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48735640

%PDF-1.6 % 1 0 obj >/OCGs[4 0 R 5 0 R 6 0 R 7 0 R]>>/Outlines 2 0 R/Pages 3 0 R/Type/Catalog>> endobj 8 0 obj >stream 2022-05-04T11:05:29-07:00 2022-05-02T18:12:27-07:00 2022-05-04T11:05:29-07:00 Appligent AppendPDF Pro 5.5 uuid:ff14d67b-b406-11b2-0a00-782dad000000 uuid:6c5a6948-1dd2-11b2-0a00-1e00285ab7ff application/pdf 48735640 Administrator Acrobat Distiller 8.1.0 (Windows) AppendPDF Pro 5.5 Linux Kernel 2.6 64bit…

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Multiplexed genome regulation in vivo with hyper-efficient Cas12a

. 2022 Apr;24(4):590-600. doi: 10.1038/s41556-022-00870-7. Epub 2022 Apr 12. Lucie Y Guo #  1   2 , Jing Bian #  3 , Alexander E Davis  4 , Pingting Liu  4 , Hannah R Kempton  3 , Xiaowei Zhang  3 , Augustine Chemparathy  3 , Baokun Gu  3 , Xueqiu Lin  3 , Draven A Rane  3 , Xiaoshu Xu  3 , Ryan M…

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CYP2D6 antibody | Anti-CYP2D6 | stjohnslabs

Host: Goat Applications: Pep-ELISA, WB Reactivity: Human Note: FOR RESEARCH USE ONLY (RUO). Short Description: Goat polyclonal antibody anti-CYP2D6 (C-Term) is suitable for use in ELISA and Western Blot research applications. Clonality: Polyclonal Conjugation: Unconjugated Isotype: IgG Formulation: 0.5 mg/ml in Tris saline, 0.02% sodium azide, pH7.3 with 0.5% bovine…

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Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites

Van Treuren, W. & Dodd, D. Microbial contribution to the human metabolome: implications for health and disease. Annu. Rev. Pathol. 15, 345–369 (2020). PubMed  Article  CAS  Google Scholar  Russell, W. R. et al. Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein. Mol. Nutr. Food…

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Director of Bioinformatics in Chicago, IL for University of Chicago (UC)

Details Posted: 03-May-22 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Hyde Park Campus Job Description: Provides technical expertise in the selection, validation, and implementation of the appropriate internal and external data analytic and bioinformatic solutions needed to analyze specimens, process and integrate data, and…

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tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data | BMC Bioinformatics

tReasure (tRNA Expression Analysis Software Utilizing R for Easy use) is a graphical user interface (GUI) tool for the analysis of tRNA expression profiles from deep-sequencing data of small RNAs (small RNA-seq) using R packages. The whole analysis workflow, including the uploading of FASTQ files of small RNA-seq, quantification of…

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FastQ_7 April 2022(1) – Copy.pptx – What is the FASTA format? The FASTA format is the “workhorse” of bioinformatics. It is used to represent sequence

the FASTA format is not “officially” defined – even though it carries the majority of data information onliving systems. Its origins go back to asoftware tool calledFastawritten byDavidLipman(ascientist that later became, and still is, the director of NCBI) andWilliam R. Pearsonof the University ofVirginia. The tool itself has (to some…

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Identification of Potential Biomarkers for Progression and Prognosis of Bladder Cancer by Comprehensive Bioinformatics Analysis

This article was originally published here J Oncol. 2022 Apr 19;2022:1802706. doi: 10.1155/2022/1802706. eCollection 2022. ABSTRACT Background. Bladder cancer (BLCA) is a highly malignant tumor that develops in the urinary system. Identification of biomarkers in progression and prognosis is crucial for the treatment of BLCA. BLCA-related differentially expressed genes (DEGs)…

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Error in SummarizedExperiment

I have installed DESeq2 version 1.36.0 samples <- colnames(txi$counts) group <- as.factor(c(“control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”, “control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”,”diet”)) coldata <- data.frame(samples, group, stringsAsFactors = F) coldata <- coldata[,c(“samples”,”group”)] coldata$samples <- factor(coldata$samples) coldata$group <- factor(coldata$group) rownames(coldata) <- sub(“fb”, “”, rownames(coldata)) all(rownames(coldata$samples) %in% colnames(txi)) all(rownames(coldata) == colnames(txi)) TRUE library(DESeq2) ddsTxi <- DESeqDataSetFromTximport(txi, colData = coldata, design =…

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‘Nobody can be forced to get vaccinated against Covid-19’: Supreme Court to Centre

The number of Covid-19 cases in India is on the rise again and as an effort, the Centre has decided to ramp up the pace of vaccination and reimpose some of the Covid-19 restrictions that were done away with after the third wave of the pandemic subsided. Amid this,…

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ggplot2 – Plot two lines on one graph on left panel and their difference on the right panel using facet_wrap or facet_grid in R

I have the following data frames: df1 <- data.frame(a= c(1:10), x= c(0.1, 0.5, 0.2, 0.1, 0, 0.23, 0.25, 0.4, 0.01, 0.2), y= c(0.3,0.01, 0.8, 0.2, 0.02, 0.14, 0.47, 0.35, 0, 0.32), name=”L1″) df2 <- data.frame(a= c(1:10), x= c(0.2, 0.25, 0.2, 0.1, 0, 0.23, 0.25, 0.4, 0.01, 0.2), y= c(0.76,0.81, 0.18,…

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Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics

Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…

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installation of qiime2 on pycharm with anaconda interperter

I’m a relatively new qiime2 (bioinformatics tool based on python language) and python user. So far, I have been using qiime2 inside a virtual machine, which is ok but not great. Since I’m taking a python course and have gotten used to work with pycharm, I’m trying to install the…

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Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Outcome of DNA sequencing, assembly, and validation In this study, initially total DNA was isolated from the finely chopped, full-grown pupa of Blepharipa sp. The NanoDrop spectrophotometer (1294 ng/μl) and the Qubit fluorometer (732.8 ng/μl) both found that the concentration of total DNA in the sample at an optimum level for mitochondrial DNA enrichment. The Tape Station profile showed…

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Y140591 – YFull YTree Info

R-Y140591 – YFull YTree Info Sample ID Country / Language Info Ref File Testing company Statistics Status YF067865 Germany R-Y140591* —— Hg38 .BAM FTDNA (Y700) 52X, 18.7 Mbp, 151 bp YF076495 Germany R-FT167842 —— Hg38 .BAM FTDNA (Y700) 49X, 18.3 Mbp, 151 bp YF067633 Germany R-FT167842 —— Hg38 .BAM FTDNA…

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r – How to keep row names when running h2o automl?

I’m performing a classification task and in particular my goal is to detect the churn of the customers of a company. I’m currently using the library lares that takes advantage of the h2o.automl() function from h2o library: aml = h2o_automl(df, y = target,max_models = 100) #run the models aml$scores_test %>%…

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Circulating cell-free mtDNA release is associated with the activation of cGAS-STING pathway and inflammation in mitochondrial diseases

Craven L, Alston C, Taylor R, Turnbull D (2017) Recent advances in mitochondrial disease. Annu Rev Genomics Hum Genet 18:257–275. doi.org/10.1146/annurev-genom-091416-035426 CAS  Article  PubMed  Google Scholar  El-Hattab AW, Adesina AM, Jones J, Scaglia F (2015) MELAS syndrome: clinical manifestations, pathogenesis, and treatment options. Mol Genet Metab 116(1–2):4–12. doi.org/10.1016/j.ymgme.2015.06.004 CAS  Article …

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Bioconductor – RAREsim

DOI: 10.18129/B9.bioc.RAREsim     Simulation of Rare Variant Genetic Data Bioconductor version: Release (3.15) Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins – either as provided by default parameters or estimated from…

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Genes looking differential abundant are not accoring to DESeq2

Genes looking differential abundant are not accoring to DESeq2 0 I have a metagenomic dataset crossing three time points from which I have mined CAZymes and am using DESeq2 to identify differentially abundant CAZymes from using trimmed mean depth generated my CoverM (very similar to Q2Q3 contig coverage). From this…

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Principal Bioinformatics Scientist I (REMOTE) job with F. Hoffmann-La Roche AG

Job Description We are seeking a committed and driven Principal Bioinformatics Scientist for our Computational Bioinformatics Research and Early Development team. We have a team of skilled bioinformatics researchers working in a highly collaborative environment with multiple internal and external teams. The work will be focused on developing novel methods…

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Research Fellow in Health and Biomedical Data Sciences job with UNIVERSITY OF SURREY

Health Sciences Research Location: Guildford Salary: £33,309 to £40,927 Post Type: Full Time Closing Date: 23.59 hours BST on Tuesday 10 May 2022 Reference: 027322 This is a rare opportunity for a talented, motivated postdoctoral fellow to work on a number of exciting health data-sciences and biomedical informatic studies. You will…

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Euro-BioImaging Bio-Hub – FAIR Image Data Steward at European Molecular Biology Laboratory (EMBL)

About the team/job Euro-BioImaging ERIC (www.eurobioimaging.eu) is a leading pan-European research infrastructure that provides the research community open access to cutting-edge imaging services. The Euro-BioImaging Bio-Hub hosted by European Molecular Biology Laboratory (EMBL) is looking for a highly motivated FAIR Image Data Steward to develop general guidelines and technically support…

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Electroporation and Electrochemotherapy in Gynecological and Breast Cancer Treatment

Review . 2022 Apr 12;27(8):2476. doi: 10.3390/molecules27082476. Affiliations Expand Affiliation 1 Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland. Free PMC article Item in Clipboard Review Zofia Łapińska et al. Molecules. 2022. Free PMC article Show details Display options Display options Format…

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Scientific Database Curator at European Molecular Biology Laboratory (EMBL)

About the team/job Metabolomics is the study of small molecule metabolites in the metabolome, which is the complete set of metabolites in a biological sample. By studying these metabolites, we can observe changes in cellular networks and biochemical pathways. This allows us to detect disease states and their progression, monitor…

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Bioinformatics Jobs in White Waltham, England

3.3 Principal Scientist – R&D Omics and Bioinformatics Slough, Berkshire, South East England, England £35,587 – £45,000 (Glassdoor Est.) Providing oversight and executing scientific activities with elements of study design and implementation, laboratory work, scientific review, coaching of junior…… 3.6 3.3 Director, High Throughput Biologics R&D Slough, Berkshire, South East…

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Unit Manager – Bioinformatics and Genomic Epidemiology

MPHI is a Michigan-based and nationally engaged, non-profit public health institute.  We are a team of teams, process and content experts, dedicated to building A world where tomorrow is healthier than today!   Title:                              Unit Manager – Bioinformatics and Genomic Epidemiology                                        $66,100 – $97,200 / Posted Thru:  4-28-22   Location: …

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Rat Model Market revenue worth USD 2.3 Billion by 2028,

Selbyville, Delaware, April 26, 2022 (GLOBE NEWSWIRE) — The rat model market value is projected to reach USD 2.3 billion by 2028, according to a new research report by Global Market Insights Inc. Growing consumption of personalized medicine and increasing number of clinical trials is expected to augment the market…

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biotechnology jobs in italy

Biotechnology Jobs: Here’re the available jobs in the biotechnology field. 96 jobs to view and apply for now with New Scientist Jobs NextPharmaJob.com is dedicated to putting job seekers looking for pharmaceutical industry jobs in touch with recruiters and employers. Find job openings from companies that are hiring now (and…

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Biomedical/BioInformatics Intern in Rockville, MD

Description Job Description: The Government Health and Safety Solutions Group within the Health group has an opening for a  Biomedical/Bioinformatics Intern. The intern will work alongside data scientists and managers and use biomedical or genomics data to inform health-related research questions. Primary Responsibilities: Under the guidance of Leidos staff, the…

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R For SEO Part 3: Data Visualisation With GGPlot2 & Wordcloud

[This article was first published on R | Ben Johnston, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don’t. R For SEO Part 3:…

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[Solved] ggplot with 2 y axes on each side and different

Sometimes a client wants two y scales. Giving them the “flawed” speech is often pointless. But I do like the ggplot2 insistence on doing things the right way. I am sure that ggplot is in fact educating the average user about proper visualization techniques. Starting with ggplot2 2.2.0 you can…

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Zydus Lifesciences : announces publication of “DREAM-ND” and “DREAM-D” Phase 3 trials of Desidustat in “American Journal of Nephrology”

Zydus announces publication of “DREAM–ND” and “DREAM–D” Phase 3 trials of Desidustat in “American Journal of Nephrology” Ahmedabad, India, 25 April 2022, Zydus Lifesciences Ltd. (formerly known as Cadila Healthcare Ltd.), a discovery-driven, global lifesciences company today announced the publication of two manuscripts detailing the DREAM-ND and DREAM-D Phase 3…

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Bioconductor – AHEnsDbs

DOI: 10.18129/B9.bioc.AHEnsDbs     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see AHEnsDbs. EnsDbs for AnnotationHub Bioconductor version: 3.10 Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species. EnsDb SQLite databases are generated separately from Ensembl MySQL databases using functions from the…

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NCBI/mweb11 – WWW Error 404 Diagnostic

NCBI/mweb11 – WWW Error 404 Diagnostic The page you requested ( h t t p : / / w w w . n c b i . n l m . n i h . g o v / g e o / q u e r y / a…

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Summary of Fusobacterium nucleatum MJR7757B, version 26.0

Summary of Fusobacterium nucleatum, Strain MJR7757B, version 26.0 Tier 3 Uncurated Database Summary: This Pathway/Genome Database (PGDB) was generated on 27-May-2018 from the annotated genome of Fusobacterium nucleatum MJR7757B, as obtained from RefSeq (annotation date: 04-APR-2017). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software…

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Merge.file do not like CAP letters – mothur bugs

Hello, I ran into this problem while running mothur on a server. mothur > merge.files(input=saraCPERF.trim.contigs.unique.good.good.filter.unique .precluster.denovo.vsearch.pick.fasta-combinedphyto.good.filter.unique.precluste r.denovo.vsearch.fasta, output=combined_saraCPERF.fasta) Unable to open combinedphyto.good.filter.unique.precluster.denovo.vsearch.fasta. Trying mothur’s executable directory combinedphyto.good.filter.unique.precluste r.denovo.vsearch.fasta. Unable to open combinedphyto.good.filter.unique.precluster.denovo.vsearch.fasta. Unable to open ▒!q▒cod.filter.unique.precluster.denovo.vsearch.fasta. Trying mot hur’s executable directory ‘qod.filter.unique.precluster.denovo.vsearch.fasta. Unable to open ‘qod.filter.unique.precluster.denovo.vsearch.fasta. free(): double free detected…

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phylogenetics – Biopython reads my tree eternally long

I have a nexus tree (1332 taxa) with a lot of additional data. When I tried to read it through tree = Phylo.read(treepath, “nexus”), my kernel got eternally loaded. If I abort the process, I get the following message: ————————————————————————— KeyboardInterrupt Traceback (most recent call last) Input In [95], in…

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Bioconductor – bladderbatch

DOI: 10.18129/B9.bioc.bladderbatch     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see bladderbatch. Bladder gene expression data illustrating batch effects Bioconductor version: 3.12 This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an…

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Molecular Modeling Software for Chemistry Market Size, Scope And Forecast

New Jersey, United States – The Molecular Modeling Software for Chemistry Market report is the ultimate tool to help industries, companies, and organizations make informed decisions for business growth. With the help of the market tactics and strategies covered here, it becomes easy for business players to maintain their position in…

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Postdoc / Research Scientist in Bioinformatics and Computational Genomics

Job Description Are you a computer geek with a strong interest in genomics? Do you want to use your computational skills to solve human diseases? At the Department of Neurology at Harvard Medical School and Brigham & Women’s Hospital, we have two vacant positions: postdoctoral fellow and research scientist in…

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Bioinformatics Analyst II – Remote in Danville, PA for Geisinger

Details Posted: 22-Apr-22 Location: Danville, Pennsylvania Type: Full Time Salary: Open Categories: Operations Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research….

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Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing

** Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing ** The NeuroGenomics and Informatics (NGI) Center lead by Dr. Carlos Cruchaga at Washington University School of Medicine is recruiting a Bioinformatics Scientist to work on Whole Genome and Whole Exome Sequencing. We are seeking an experienced, self-motivated, self-driven scientist…

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Lenvatinib+Pembrolizumab Adverse Reactions in Advanced RCC Characterized

Investigators have characterized the adverse reactions (ARs) resulting from the use of lenvatinib plus pembrolizumab in patients with advanced renal cell carcinoma (aRCC) as well as how these ARs were managed. “Clinicians play a critical role in the prompt identification and management of ARs in patients with aRCC treated with…

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Global KRAS Inhibitors Market & Clinical Trials Forecast Report to 2028 – ResearchAndMarkets.com

DUBLIN–(BUSINESS WIRE)–The “Global KRAS Inhibitors Market & Clinical Trials Forecast 2028” report has been added to ResearchAndMarkets.com‘s offering. The advancement in clinical research has led to the identification of several oncogenes that are generally mutated in cancers. Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) is the most frequently mutated…

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Unable to open pdf file of volcano plots created using many group comparisons from EnhancedVolcano package in R

Hi, I am working with a dataframe in R containing the quantitative data and trying to plot a volcano plot using library(EnhancedVolcano) package. I am currently analyzing by subsetting based on corresponding matching pairs of “Coef” and “P.value” obtained from limma (for instance; Coef.HC_6h_vs_0h and P.value.HC_6h_vs_0h) individually and export the…

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Manager of Bioinformatics in Chicago, IL for University of Chicago (UC)

Details Posted: 22-Apr-22 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Hyde Park Campus Job Description: Leads a team of bioinformaticians and provides technical guidance for the team to follow best practices and deliver data production timely. Collaborates cross-functionally with our user services, software engineering,…

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The modules are not clustered together after WGCNA

The modules are not clustered together after WGCNA 0 I am running WGCNA and trying to visualize the gene network as TOM plot. Rather than using the native function in the package, I am looking for plotting it out by ggplot. The main reason is I would like to also…

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Endometriosis-related functional modules and hub genes

Introduction Endometriosis (EMS) is a chronic gynecological disease defined as implantation and periodic growth of the endometrial glands and stroma outside the uterine cavity, causing chronic pelvic pain, severe dysmenorrhea, and infertility in 10% reproductive-age women, among which the infertility rate is approximately 30–50%.1,2 Surgical excision is commonly used for…

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Creating a non-stacked area plot in an easier way (ggplot2) : rprogramming

Hello! I don’t actually know what this type of chart would be called, but I essentially want to create a non-stacked area chart, ideally through one ggplot2 command. I’m able to create pretty much exactly what I’m after through simply calling geom_area() twice, as in the picture below. Here’s the…

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r – Change axis ranges for a ggplot based on a Predict object (rms package)

Unusually, the Predict class of rms has its own S3 method for ggplot, which automatically adds position scales, coordinates and geom layers. This makes it easier to plot Predict objects, but limits extensibility. In particular, it already sets the y limits via a CoordCartesian, which over-rides any y axis scales…

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docker compose – How to enable authentication via openLDAP on JupyterHub without SSL certificate?

I am trying to create a JupyterHub that uses an LDAP to authenticate users. The JupyterHub is working but when I am trying log on the web page show a Error 500. I must clarify that when I tried it with the PAM method it worked without problems, but when…

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C1qBP antibody [GT1250] | Axil Scientific

This website uses cookies to ensure the best experience. By continuing, you agree to our privacy policy. × Product successfully added to quote! × There are items in your quote. Brand: Reference GTX02847 Brand GeneTex Application IHC-PWB Storage Conditions Store as concentrated solution. Centrifuge briefly prior to opening vial. For…

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RNA Interference (RNAi) Drug Delivery Market Analysis 2022: Industry Overview, Growth, Trends, Opportunities and Forecast Till 2027

 According to IMARC Group’s latest report, titled “RNA Interference (RNAi) Drug Delivery Market: Global Industry Trends, Share, Size, Growth, Opportunity and Forecast 2022-2027”, the global market reached a value of US$ 54.74 Billion in 2021. RNA interference (RNAi) drug delivery is a fundamental cellular mechanism that studies gene functions in…

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TREEFROG THERAPEUTICS LAUNCHES A $100,000 RESEARCH GRANT IN REGENERATIVE MEDICINE

Bordeaux, France / April 19th, 2022 – TreeFrog Therapeutics, a biotechnology company aimed at making safer, more efficient and more affordable cell therapies based on induced pluripotent stem cells (iPSCs), today announced the launch of The Stem Cell SpaceShot Grant, a $100,000 research funding in the field of stem cell…

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A114 – YFull YTree Info

R-A114 – YFull YTree Info SNPs currently defining R-A114 FGC78244     A114(H)     H Sample ID Country / Language Info Ref File Testing company Statistics Status YF067576 France (Ille-et-Vilaine) R-A114* —— Hg19 .BAM Dante Labs 12X, 23.0 Mbp, 151 bp YF088360 United States (Virginia) R-CTS4466* —— Hg38 .BAM FTDNA (Y700)…

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How to install SageMath in Ubuntu Linux?

SageMath is a free and open-source software for mathematical computation. It is built on top of many existing open-source libraries which include NumPy, SciPy, Matplotlib, SymPy, Maxima, etc. SageMath provides a command-line interface, browser-based notebooks, and tools for embedding formulas in other documents. Its syntax is similar to Python. In…

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Whole-genome analysis of coxsackievirus B3 reflects its genetic diversity in China and worldwide | Virology Journal

Song Y, Zhang Y, Han Z, Xu W, Xiao J, Wang X, et al. Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity. Virus Evol. 2020;6:2. doi.org/10.1093/ve/veaa048. Article  Google Scholar  Chen J, Han Z, Wu H, Xu W, Yu D, Zhang Y. A large-scale outbreak…

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Still doubts over embryo selection based on PGT for polygenic conditions

Advances in genomic technologies continue to expand the possibilities of PGT. In a preclinical research study recently published in Nature Medicine, scientists from Silicon Valley-based genetic testing companies have examined the potential of using PGT to predict complex polygenically inherited conditions in human embryos. While the authors present interesting data,…

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Medical Alert System/Personal Emergency Response System Market Size And Forecast

New Jersey, United States – Medical Alert System/Personal Emergency Response System Market Research Report provides you with detailed and accurate analysis to strengthen your position in the market. It provides the latest updates and powerful insights on the Medical Alert System/Personal Emergency Response System industry to help you improve your business…

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python – How are paths meant to be denoted on for Biopython on mac?

I am trying to run a basic biopython script to rename sequences within a fasta file. I have only ever ran this on a server; i am trying to do it on my macbook but I can’t work out what the correct path to the file should be. on the…

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Can Differential Isoform expression analysis can be performed using DESeq2 package

Can Differential Isoform expression analysis can be performed using DESeq2 package 0 @03ddb485 Last seen 9 hours ago India Hello, I am want to perform differential isoform expression (DIE) analysis for RNAseq data from human. Can I use DESeq2 for this by inputting the transcript level abundance and getting differential…

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Kaggle Machine Learning

In this article, we’ll learn step by step an entire process of machine learning to solve a challenge in Kaggle Competition and make a submission. We’ll explore through Kaggle Competition joining, Data Exploration, Feature Engineering, Model Training, Testing, Scoring, and Evaluation. Then, we’ll go ahead and submit our result to…

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