Tag: query

AWS launches Amazon Omics for precision medicine

To enhance clinical insights at the point of care and help identify the best treatment or prevention options for patients, Amazon Web Services has launched a service that utilizes artificial intelligence (AI), machine learning, and other AWS and partner products and services to run IT-heavy bioinformatics workflows.  WHY IT MATTERS…

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query regarding error in installation of “goseq” R bioconductor package

query regarding error in installation of “goseq” R bioconductor package 0 @6d5973d2 Last seen 19 hours ago India I am trying to install “goseq” Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2 I getting many error messages which are…

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Characterization, genome analysis and genetic tractability studies of a new nanocellulose producing Komagataeibacter intermedius isolate

Isolation, characterization and classification of BC-producing strain Isolation of single clones from CaCO3 halo zones in Glucose-Yeast Extract-Calcium carbonate agar and iterated subculturing in HS-Glu agar resulted in enrichment of an isolate with beige-coloured, smooth-edged and umbonate shaped colonies characteristics (Fig. S1A). The isolate is hereafter called ‘ENS15’. Under 100X magnification,…

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Searching for homologous sequences of small peptides in several species

BLASTP – Searching for homologous sequences of small peptides in several species 0 Hello! I now have some protein sequences of a number of species (chicken, human, mouse, …). I want to use BLASTP to find the homologous sequence of a small peptide “KPWLRVALCPG” in these species. For the convenience…

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How to retrieve all genes of interest from GenBank?

How to retrieve all genes of interest from GenBank? 1 Hello Bioinformagicians! My goal is to create a phylogenetic tree using mitochondria genes of ticks. I’ve recently use genes taken from Refseq complete genomes. However, I want to include gene sequences that may not be part of complete genomes. How…

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Kaggle Online Courses | Free Online Certification Courses

Kaggle is a platform for learners and competitors in data science and machine learning. Kaggle is maintained as a subsidiary of Google LLC. It was Headquartered in San Francisco, USA. It is famous for data science learning and competitions. It was started in April in the year 2010. Why free…

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Senior Clinical Bioinformatics Scientist – Medical Center, New York, United States

Senior Clinical Bioinformatics Scientist 525626 Medical Center Institute for Genomic Medicine Full Time Grade 104 Job Type: Officer of Administration Bargaining Unit: Regular/Temporary: Regular End Date if Temporary: Hours Per Week: 35 Salary Range:   Position Summary The Precision Genomics Laboratory (PGL), a partnership between the Department of Pathology and…

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bcftools view remove (.) id

Hello I have a txt file that consists from CHROM,ID,POS, REF and ALT ( 48 variants ) I want to subset this txt with original VCF to make a new VCF I try to use bcftools using this query bcftools view -T variants.txt mydata.vcf > variant1.vcf but the problem ,…

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React & REST APIs: End-To-End TypeScript Based On OpenAPI Docs

When you work on a React & TypeScript project that fetches data from a REST API, keeping your data types in sync can be problematic. You obviously can create all the types on your frontend by hand. But this is a tedious and error-prone process. You might get a type…

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New Algorithms That Harnessed Protein-folding Power in 2022

Big pharma companies have been researching protein folding for a long time now. Discoveries and innovations in the field can revolutionise the development of drug and other biological advancement. Recently, the development of the COVID-19 vaccine was also supported by tackling this issue.  Protein folding prediction process involves a combination…

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Bioinformatics Services Market is Expected to Record the Massive Growth, with Prominent Key Players Illumina, Thermo Fisher Scientific, Eurofins Scientific

New Jersey, United States, Oct 17, 2022 /DigitalJournal/ Bioinformatics is a multidisciplinary scientific field where biologists, physicians, computer scientists, mathematicians, physicists, and bioinformaticians work together to analyze, interpret and understand the growing amount of biological data. Growing implementations of bioinformatics services in countless end-use industries such as bioremediation, forensics, consumer…

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UCSC Genome Browser | Encyclopedia MDPI

1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…

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Removing metadata rows containing NA values in GRanges

Removing metadata rows containing NA values in GRanges 1 @3a63554b Last seen 20 hours ago Singapore I’m looking for promoters for protein coding transcripts in GRanges, and I end up with lots of NA values in my protein_id metadata column. Is there a way to remove the rows corresponding to…

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Computational Biology Software Market Experience Increasing Demand by 2029

“ As part of an worldwide Computational Biology Software market research project, a detailed analysis of the company profiles of important industry suppliers is carried out. Computational Biology Software research identifies the most successful manufacturers worldwide and gives data on their sales, income, and pricing in addition to other relevant…

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Institut Pasteur de Dakar hiring Bioinformatics Analyst in Dakar, Senegal

We are looking for an enthusiastic and motivated bioinformatician to join the Epidemiology, Clinical Research, and Data Science department at the Institut Pasteur de Dakar. The selected candidate will develop and apply bioinformatics methods to support multiple projects in the area of next-generation sequencing and -omics. Minimum qualification Bachelor’s degree…

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Comment: How to resolve a ValueError: Multiple 'HD' Lines are not permitted when I run Ci

I tried your suggestion **samtools view -H qname_unknown_circle.bam** and the output result is like this: yu@root:~$ samtools view -H qname_unknown_circle.bam @HD VN:1.5 SO:queryname @SQ SN:chr1 LN:248956422 @SQ SN:chr10 LN:133797422 @SQ SN:chr11 LN:135086622 ………(Many lines like this ‘@SQ SN:chrxx LN:xxxx’ are omitted) @SQ SN:chrY_KI270740v1_random LN:37240 @HD VN:1.5 SO:unsorted GO:query @PG ID:bwa…

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Service Procurement Market Growth Challenges (2022-2028)

“ The global Service Procurement market is being driven by a surge in demand for precise technology, as well as rising government steps to promote efficient procedures that raise productivity and benefit industrial players. The introduction of rules controlling the use of new technology such as drones and AI, on…

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ggplot2 – Query On geom_raster When Creating Maps

I have a code for creating a map that works. I am now trying to add a raster layer with salinity gradient. I have been following a couple of tutorials and my current approach goes as follows: # Loads .TIF file ~ Salinity <- stack(“Present.Surface.Salinity.Mean.tif”) # Converts .TIF into dataframe…

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a new and efficient development model, to achieve code and API separation, efficient development, development must see!!!

什么是openapi 3.0 OpenAPI 3.0.0 是 OpenAPI The first official version of the specification,因为它是由 SmartBear Software 捐赠给 OpenAPI Initiative,并在2015年从 Swagger 规范重命名为 OpenAPI 规范. 介绍: OpenAPI 规范(OAS),is to define a standard、programming language-independentRESTful API的规范.OpenAPI Specifications enable both humans and computers to“Do not contact with any program source code and documentation、Does not monitor network…

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Kaggle’s Titanic Disaster Survivor Prediction

Check out our first part of the Titanic blog series where we explore the Kaggle Titanic Disaster survivor prediction notebook and convert it into a #Kubeflow pipeline using Kale! – arrik.to/3A0mAAX #MachineLearning #DataScience #MLOps Kubeflow Pipelines: Kaggle’s Titanic Disaster Survivor Prediction – Part 1 |… Home Check out our first…

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Gene Amplification Technologies Market Analysis Report 2022 –

Acumen Research and Consulting has announced the addition of the “Gene Amplification Technologies Market” report to their offering. The Gene Amplification Technologies Market Report 2030 is an in depth study analyzing the current state of the Gene Amplification Technologies Market. It provides brief overview of the market focusing on definitions,…

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I have a query regarding differential gene expression using limma-voom.

I have a query regarding differential gene expression using limma-voom. 1 @28946033 Last seen 1 day ago India I used the following pipeline for RNA Seq Analysis Fastq-Trimmomatic- Hisat2(gtf file was annotated)-featurecounts After featurecounts I tried to do limmavoom, but I get error saying this An error occurred with this…

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Electroporation Systems Market 2022 Comprehensive Analysis, Growth And Forecast to 2030 | Biotron Healthcare, Merck, Eppendorf

Key Companies Covered in the Electroporation Systems Research are Biotron Healthcare, Merck, Eppendorf, Thermo Fisher, Bio-Rad, MaxCyte, Harvard Apparatus, Biogenuix and other key market players. The Electroporation Systems market revenue was $$ Million USD in 2016, grew to $$ Million USD in 2022, and will reach $$ Million USD in…

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Electroporation Systems Market 2022 Comprehensive Analysis, Growth And Forecast to 2030 | Biotron Healthcare, Merck, Eppendorf | Taiwan News

Key Companies Covered in the Electroporation Systems Research are Biotron Healthcare, Merck, Eppendorf, Thermo Fisher, Bio-Rad, MaxCyte, Harvard Apparatus, Biogenuix and other key market players. The Electroporation Systems market revenue was $$ Million USD in 2016, grew to $$ Million USD in 2022, and will reach $$ Million USD in…

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Get gene names from rs SNP ids for mmusculus_gene_ensembl

Get gene names from rs SNP ids for mmusculus_gene_ensembl 1 I have mouse data with an old mapping from rs SNP IDs to base pair position and chromosome. I would like to query Ensembl to get the genes and then the gene annotations for the rs SNP IDs in my…

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Check Post, Qualifications, Age, and How to Apply Here

ICAR- IARI Recruitment 2022: Check Post, Qualifications, Age, and How to Apply Here ICAR- IARI Recruitment 2022: Indian Council of Agricultural Research (ICAR) has invited applications for interviews for the recruitment of Senior Research Fellow (ONE post) for ICAR­NASF funded project and Young Professional-II (ONE post) for ICAR-CABin funded project,…

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Data Communication Based on MQTT in a Polymer Extrusion Process

This work proposes a flexible method for data communication between a film extrusion system and monitoring devices based on a message protocol called Message Queuing Telemetry Transport (MQTT). The protocol in this work allows building a flexible data communication structure for a Polymer processing machine by employing a publisher subscriber…

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Senior Bioinformatics Research Scientist – Computational Biology/Data Science, remote

Job Description Look for more than answers. At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the Diagnostic Lab in the US. For those joining us, we offer exciting and fast-moving career opportunities where you can…

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New ‘Ramp Atlas’ Aims to Improve Understanding of Gene Expression

CHICAGO – A first-of-its-kind atlas of “ramp sequences” near the 5′ end of highly expressed genes promises to help researchers better understand gene expression and disease development. Bioinformaticians and computational biologists at the University of Kentucky and Brigham Young University recently released the Ramp Atlas, a compendium of 18,388 tissue-…

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German Cancer Research Center in the Helmholtz Association (DKFZ) hiring Postdoc in Bioinformatics, Medical Informatics or Biostatistics in Brussels, Brussels Region, Belgium

Offer DescriptionThe German Cancer Research Center is the largest biomedical research institution in Germany. With approximately 3,000 employees, we operate an extensive scientific program in the field of cancer research. Together with university partners at seven renowned partner sites, we have established the German Cancer Consortium (DKTK). For the partner…

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Open Rank Bioinformatics Software Engineer I and Bioinformatics Engineer II in Baltimore, MD for University of Maryland, Baltimore

Open Rank Bioinformatics Software Engineer I and Bioinformatics Software Engineer II The Institute for Genome Sciences (IGS), Informatics Resource Center, is recruiting for a Open Rank Bioinformatics Software Engineer I and Bioinformatics Software Engineer II position. This position will be filled as either the Bioinformatics Software Engineer I or II.IGS…

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Resolved: Adding a legend to ggplot

Question: I have the below dataset; Player Goals Shots Regan Charles-Cook 10 32 Tony Watt 9 36 Bruce Anderson 8 26 Liam Boyce 8 44 Kyogo Furuhashi 8 31 Alfredo Morelos 8 80 Christian Ramirez 8 41 Liel Abada 7 57 Martin Boyle 7 43 Kevin van Veen 7 45…

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Lh3 Minimap2 Issues

Issue Title State Comments Created Date Updated Date Mapping reads against multi references. Any proposition? open 0 2022-06-28 2022-06-30 Inversion between tandem repeats yields misalignment closed 1 2022-06-21 2022-06-30 use minimap2 to extract mitochondrial reads from genome assembly open 0 2022-06-20 2022-06-30 Asking for #301 to be reopened closed 0…

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ARCH= -gencode arch=compute for NX: – Jetson Xavier NX

hi,i am working on jetson Xavier NX box,i updated to jetpack 5.0.1 and deepstream6.1 right now.before i setup ARCH= -gencode arch=compute 72 for NX to train some models.but i cmake another file yesterday it detected arch-gencode 75!so i am confuse right now, should i setup 72 or 75 for jetson…

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Induzierte pluripotente Stammzellen (IPSCs) Marktanteil, Analyse der wichtigsten Wettbewerber, Prognose bis 2028

Der Induzierte pluripotente Stammzellen (IPSCs) Market“-Forschungsbericht umfasst umfassende Daten zu vorherrschenden Trends, Treibern, Wachstumschancen und Einschränkungen, die die marktverändernden Aspekte der globalen Industrie variieren können. Dieser Bericht bietet eine eingehende Analyse der Marktsegmentierung, die Produkte, Anwendungen und geografische Analysen enthält. Der globale Induzierte pluripotente Stammzellen (IPSCs)-Marktbericht bietet eine genaue Beobachtung…

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Ubuntu Manpage: bamfillquery – fill query sequences into BAM files

Provided by: biobambam2_2.0.179+ds-1_amd64 NAME bamfillquery – fill query sequences into BAM files SYNOPSIS bamfillquery [options] <in.bam queries.fasta >out.bam DESCRIPTION bamfillquery reads a SAM/BAM/CRAM file and a FastA file, copies the sequences found in the FastA file into the query sequence field of the SAM/BAM/CRAM file and writes the resulting data…

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How To Download Geo Data? Update New

Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Images related to the topicBioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics…

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Bioinformatics Analyst at Dana-Farber Cancer Institute in 450 Brookline Ave, Boston, MA

Located in Boston and the surrounding communities, Dana-Farber Cancer Institute is a leader in life changing breakthroughs in cancer research and patient care. We are united in our mission of conquering cancer, HIV/AIDS and related diseases. We strive to create an inclusive, diverse, and equitable environment where we provide compassionate…

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python 3.x – PySpark on Jupyterhub K8s || Unable to query data || Class org.apache.hadoop.fs.s3a.S3AFileSystem not found

Pyspark Version: 2.4.5 Hive Version: 1.2 Hadoop Version: 2.7 AWS-SDK Jar: 1.7.4 Hadoop-AWS: 2.7.3 When I am trying to show data I am getting Class org.apache.hadoop.fs.s3a.S3AFileSystem not found while I am passing all the information which all are required. I passed all three for this config fs.s3.aws.credentials.provider org.apache.hadoop.fs.s3a.BasicAWSCredentialsProvider com.amazonaws.auth.InstanceProfileCredentialsProvider com.amazonaws.auth.EnvironmentVariableCredentialsProvider…

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React Query Codegen from OpenAPI

Rapini is a new tool that can generate custom React Query hooks using OpenAPI (Swagger) files. The Command Line Interface (CLI) tool will take a path to an Open API file and generate a package that includes react hooks, typescript types and axios http requests – and this package is…

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a strange pattern of repetitive summits

Problem with the output of Deeptools PlotProfile: a strange pattern of repetitive summits 0 Hi! I am trying to plot DNA binding profiles of my ChIP-seq bw files using Deeptools plotProfile. I generated the matrix using the computeMatrix reference-point. I used some publicly available bed files as my regions of…

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Metagenomic Sequencing Market Size And Forecast

New Jersey, United States – The Verified Market Reports released the latest competent intelligence market research report on the Metagenomic Sequencing Market, The report aims to provide a thorough and accurate analysis of the Metagenomic Sequencing market, taking into account market forecast, competitive intelligence, technical risks, innovations, and other pertinent data. Its…

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Detailed differences between sambamba and samtools

3 month , My first post in the new student group , The false-positive mutation appears because duplicates mark Not enough ?, Tells the story of supplementary read It won’t be GATK MarkDuplicates Marked as duplicates The problem of . after , In response to this question , I began…

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Computational Biology Software Market Worldwide Industry Share 2022-2028

“ The report studies the key segments in global Computational Biology Software industry, their growth in past few years, profiles and market sizes of individual segments, and gives a detailed overview of the profiles of various segments. The report also presents key products and various other products in the global…

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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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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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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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Database Administrator at European Molecular Biology Laboratory (EMBL)

About the team/job In this role you will join an established Database team of database administrators in order to support the ongoing database operations. The main duties for this post are: DBA of MySQL and MongoDB.The Database Team provides day-to-day Database Administration support , database performance tuning and query optimization…

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BlastX through Biopython

BlastX through Biopython 0 I have an unknown gene segment in the Human_gene.txt file and I want to run blastx (translated nucleotide) using the blast module of Biopython by making the E-value threshold 0.0001 and displaying the match result of 50 residues of query and subject. I am trying this…

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Corporate Volunteering Platform Professional Market Records a Significant Growth by 2029

“ A comprehensive appraisal of the worldwide Corporate Volunteering Platform Professional market agglomerates basically engaged scientific outcomes and noteworthy data taking care of the vital necessities of the report peruses including market members across the worldwide Corporate Volunteering Platform Professional market, financial backers and business visionaries looking for profoundly conclusive…

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Bioinformatics Software Professional Market Records a Significant Growth by 2029

“ A comprehensive appraisal of the worldwide Bioinformatics Software Professional market agglomerates basically engaged scientific outcomes and noteworthy data taking care of the vital necessities of the report peruses including market members across the worldwide Bioinformatics Software Professional market, financial backers and business visionaries looking for profoundly conclusive examination result…

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Senior Research Associate/Principal Research Associate, Bioinformatics job with Vedanta Biosciences

Title: Senior Research Associate/Principal Research Associate, Bioinformatics Location: Cambridge, MA, or up to 100% remote Reports to: Scientist I, Bioinformatics The Role: We are looking for a bioinformatician/computational biologist to support the Research and Development team in the maintenance and querying of an existing laboratory information management system (LIMS), construction…

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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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Postdoctoral Research Fellow in Bioinformatics/Computational Biology

Details Posted: 27-Apr-22 Location: Boston, Massachusetts Salary: Open Categories: Staff/Administrative Internal Number: 2022-27118 Located in Boston and the surrounding communities, Dana-Farber Cancer Institute brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with…

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NcbiblastpCommandline alignment results are different from blast webpage

What you are trying to do is fairly simple, and you are complicating it by: 1) not providing your sequences so that someone can reproduce your attempt; 2) giving a result in a form that is impossible to read. Be honest, can you make any sense of the result you…

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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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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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Bioinformatics Salary Entry Level at Level

Bioinformatics Salary Entry Level. Similar to any other job, their salary will increase as they gain experience. What is the average salary of a bioinformatics scientist? Senior Software Engineer from www.dreamjobs.lk $31,220 to $37,970 per year. The estimated base pay is $109,228 per year….

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Digital Identity Solutions Market In-Depth Analysis including Development Strategy, Regional Analysis, Key Segmentation by Major Companies like IDEMIA, ForgeRock, Imageware Systems, Jumio, NEC, Samsung SDS

“ The global Digital Identity Solutions Market is an information rich representation of the current market developments that echo upward spike in growth numbers. Our team of research experts at Adroit Market Research has relied upon dedicated primary and secondary research methodologies to make accurate deductions of the market developments,…

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Nucleic Acids Research Papers on DAVID Update, ChIP-Atlas, RNA Splicing Assay

Researchers at the Frederick National Laboratory for Cancer Research and the National Institutes of Health describe a 2021 update to the bioinformatics tool DAVID, designed for functional annotation and functional gene enrichment analyses. Along with updates to annotation types and other “Knowledgebase” features, the latest version of the DAVID Gene…

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Qiime2 Exclude Seqs with FASTQ as query data.

Qiime2 Exclude Seqs with FASTQ as query data. 0 Hello, I am working with FASTQ files and I want to filter them based on the alignment with references sequences in FASTA format. I decided to use QIIME2 for this. So I imported both FASTA and FASTQ files to the required…

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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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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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Using QCTOOL v2 to process UK Biobank .bgen files

Using QCTOOL v2 to process UK Biobank .bgen files – why so slow? 0 I’m currently using QCTOOL v2 to process imputed .bgen files from UK Biobank, however they seem to be processing very slowly. Is this normal? My command is pretty basic; I’m filtering out a list of SNPs…

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Single cell database scrna dB for bioinformatics database development (1)

Single cell database construction High quality integrated single cell database If readers just want to get a ready-made single-cell database with rich content and add it to their own PC or linux The server , You can skip the following detailed theoretical tutorial Database download link : Click to download…

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Mapping back 3 sets of reads/sample with minimap2

I used FaQC to qc my raw fastqs before assembling. That program (and perhaps others) outputs properly paired Forward and Reverse fastqs, as well as an unpaired fastq file for each sample. I used the all 3 for each single sample assembly. Since minimap2 only allows for 2 query files,…

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GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

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How to edit a SAM file using pysam

How to edit a SAM file using pysam 0 Dear all – I have a template sam file and I want to change one of the columns (template_length) and replace it with a new value. The new value is a quick mathematical operation. template sam file: @HD VN:1.0 SO:unsorted @SQ…

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What is ClustalW? Tutorial of How to Use ClustalW

Share Tweet Share Share Email ClustalW is a computer tool of significant importance in bioinformatics. Primarily, biologists and statisticians used it for multiple sequence alignment. Many versions of ClustalW over the development of the algorithm are available now. How to perform a search on ClustalW? ClustalW homepage 1. Go to…

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RSQLite: binding sets and scalars in the same select query

Why do you specify y = I(list(7,6)) instead of y=c(6,7)? This seems to work: dbGetQuery (c, “select * from tst where x = ? and y in (?)”, data.frame(x=1, y=c(7,6))) You might be looking for expand.grid. dbGetQuery (c, “select * from tst where x = ? and y in (?)”,…

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Introduction to the BLAST Suite and BLASTN | Michael Agostino

In Chapter 2 we learned how to search databases with text queries. All of these were exact matches—that is, we were expecting to find the exact accession number or exactly spelled words. In this chapter, a much harder database-searching problem is introduced. How do you find matches when your query…

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BLASTn using R

BLASTn using R 0 Hello, I have around 2000 DNA nucleotide sequences (60 bases long) stored in each row in an excel sheet. I want to run BLAST over each one of them individually and extract the “Description” of the first hit. Like for Example: Suppose on NCBI BLAST website…

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“No such file or directory: ‘test.xml”

Biopython NcbiblastpCommandline not working: “No such file or directory: ‘test.xml” 0 from Bio.Blast.Applications import NcbiblastpCommandline blastp=r”C:\NCBI\blast-BLAST_VERSION+\bin\blastp.exe” blastp_cline = NcbiblastpCommandline(blastp, query=r”C:/NCBI/blast-BLAST_VERSION+/bin/test.fasta”, db=r’C:/NCBI/blast-BLAST_VERSION+/bin/bos_protein.fasta’, outfmt=5, evalue=0.00001, out=r”C:/NCBI/blast-BLAST_VERSION+/bin/test.XML”) blastp_cline from Bio.Blast import NCBIXML with open(“test.XML”) as result_handle: E_VALUE_THRESH=0.01 blast_records = NCBIXML.parse(result_handle) blast_record = NCBIXML.read(result_handle) for alignment in blast_record.alignments: for hsp in alignment.hsps: if hsp.expect…

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From scientific name to taxonomy information entrez

From scientific name to taxonomy information entrez 1 Hi all, I have a txt file with a list of scientific names of plants and I would like to obtain a final file with taxonomy information. For example, if one of my organism is Acalypha hispida, I would like to obtain…

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AlphaFold, GPT-3 and How to Augment Intelligence with AI

This is the first post in a two-part series. Read Part 2 here. Around the same time that Alan Turing was shaping his theories of machine intelligence in Manchester, another future giant of the computing world, Douglas Engelbart, was developing an alternative computing paradigm over 5,000 miles away in…

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Google Researchers Use Machine Learning Approach To Annotate Protein Domains

Source: www.nature.com/articles/s41587-021-01179-w.epdf Proteins play an important part in the construction and function of all living organisms. Each protein is made up of a chain of amino acid building blocks. Much like an image might have numerous things, a protein can have multiple components, known as protein domains. Researchers have been…

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Text string using Biopython – Stack Overflow

I’m using Biopython in my code and i need to extract the abstract out of articles. For searching the article I’m using the function: def search(query): Entrez.email=”your.email@example.com” handle = Entrez.esearch(db=’pubmed’, sort=”relevance”, retmax=’20’, retmode=”xml”, term=query) results = Entrez.read(handle) return results I’m looking for the simpliest way to get the text as…

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Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

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Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics

We implemented a metagenomic DNA sequencing methodology to unbiasedly detect microbial species in CSF samples from patients with CNS symptoms in which a pathogen or EBV had been detected (Additional 3: Table 1). Samples positively identified with pathogen-specific quantitative PCR (qPCR), 16S rRNA gene sequencing or bacterial/mycotic culture in CSF…

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biopython – How to blastp with fasta file that contains ~50 sequences

I’m trying to blastp multiple aminoacids sequences using biopython. I just can’t seem to get it right and i cant figure out the handbook for how to do this. I have come up with the following: open(“proteins_PROT.fasta”,”r”) from Bio.Blast.Applications import NcbiblastpCommandline cline = NcbiblastpCommandline(query=”proteins_PROT.fasta”, db=”nr”, evalue=0.001, remote=True, ungapped=True) NcbiblastpCommandline(cmd=’blastp’, query=”proteins_PROT.fasta”,…

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peroxisomal multifunctional enzyme type 2-like, maker-scaffold366_size194251-snap-gene-0.19 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of peroxisomal multifunctional enzyme type 2-like vs. L. salmonis genes Match: EMLSAG00000010112 (supercontig:LSalAtl2s:LSalAtl2s668:190059:194758:1 gene:EMLSAG00000010112 transcript:EMLSAT00000010112 description:”augustus_masked-LSalAtl2s668-processed-gene-1.1″) HSP 1 Score: 102.064 bits (253), Expect = 2.195e-25Identity = 65/191 (34.03%), Postives = 101/191 (52.88%), Query Frame = 0 Query: 134 GKVALVTGAGGGLGKAYALLLASRGASVVVNDLGGSRTGEGQSSKAADEVVNEIRQKGGKAV—–GNYDSVEDGEAVIKTALDNFGRIDIVINNAGILRDRSIGRTSDSDWDLVQKVHLRGAFQVIRAAWPHMKKQKYGRIINTSSVAGIFGNFGQSNYSSAKAGLIGLTSTLAIEGERSGIQANVIVP 319 GKVAL+TGA G+G++ A+L A…

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use tcgabiolinks package to download TCGA data

TCGA Data download in terms of ease of use ,RTCGA The bag should be better , And because it’s already downloaded data , The use is relatively stable . But also because of the downloaded data , There is no guarantee that the data is new .TCGAbiolinks The package is…

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Substitute variables in an expression in Sagemath

Somewhat similar to this question, I was trying to evaluate a Boolean expression given the right hand side variables in Sage. For simplicity, say, my Boolean expression is, $y=x_0+x_1$. For each of $(x_0,x_1) in {(0,0),(0,1),(1,0),(1,1)}$, I want to evaluate $y$. This is the basic code block to get started. Note…

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How to Build a Code Search Tool Using PyTorch Transformers and Annoy | by Youness Mansar | Feb, 2022

Leveraging joint text and code embeddings for search. Modified from Photo by Markus Winkler on Unsplash Did you ever look for a code snippet on google because you were too lazy to write it yourself? Most of us did! Then how about building your own code search tool from scratch?…

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Postdoctoral Fellowship in Bioinformatics/Statistics – UN Jobs Vacancies Tenders

*Applications may be reviewed on a rolling-basis and this posting could close before the deadline. ARS Office/Lab and Location: A postdoctoral fellowship in bioinformatics/statistics is currently available with the U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center located in New Orleans, Louisiana. Research Project: Food allergy costs the US $25…

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A mammalian methylation array for profiling methylation levels at conserved sequences

Designing the mammalian methylation array The CMAPS algorithm is designed to select a set of Illumina Infinium array probes such that for a target set of species many probes are expected to work in each species (see “Methods” section). Array probes are sequences of length 50 bp flanking a target CpG…

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AWS IoT Core Integration with NVIDIA DeepStream error in make command – #3 by AnamikaPaul – DeepStream SDK

Please provide complete information as applicable to your setup. • Hardware Platform (Jetson / GPU) Jetson nano• DeepStream Version 6.00• JetPack Version (valid for Jetson only)• TensorRT Version• NVIDIA GPU Driver Version (valid for GPU only)• Issue Type( questions, new requirements, bugs)• How to reproduce the issue ? (This is…

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Variant #0000726648 (NC_000017.10:g.7100169G>A, ACADVL(NM_000018.3):c.-23135G>A) – Global Variome shared LOVD

Variant #0000726648 (NC_000017.10:g.7100169G>A, ACADVL(NM_000018.3):c.-23135G>A) Chromosome 17 Allele Unknown Affects function (as reported) Effect unknown Affects function (by curator) Not classified Classification method – Clinical classification VUS DNA change (genomic) (Relative to hg19 / GRCh37) g.7100169G>A DNA change (hg38) – Published as DLG4(NM_001321075.2):c.990C>T (p.G330=) ISCN – DB-ID DLG4_000038 Variant remarks VKGL data sharing initiative Nederland Reference – ClinVar ID – dbSNP ID – Origin CLASSIFICATION record Segregation – Frequency – Re-site –…

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Variant #0000803285 (NC_000007.13:g.92730753A>G, SAMD9(NM_017654.3):c.4658T>C) – Global Variome shared LOVD

Variant #0000803285 (NC_000007.13:g.92730753A>G, SAMD9(NM_017654.3):c.4658T>C) Chromosome 7 Allele Unknown Affects function (as reported) Effect unknown Affects function (by curator) Not classified Classification method – Clinical classification VUS DNA change (genomic) (Relative to hg19 / GRCh37) g.92730753A>G DNA change (hg38) – Published as SAMD9(NM_017654.3):c.4658T>C (p.I1553T), SAMD9(NM_017654.4):c.4658T>C (p.I1553T) ISCN – DB-ID SAMD9_000024 See all 3 reported entries Variant remarks VKGL data sharing initiative Nederland Reference – ClinVar ID – dbSNP ID – Origin CLASSIFICATION…

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[slurm-users] Issues upgrading db from 20.11.7 -> 21.08.4

Hello! I’m trying to test an upgrade of our production slurm db on a test cluster. Specifically I’m trying to verify a update from 20.11.7 to 21.08.4. I have a dump of the production db, and imported as normal. Then firing up slurmdbd to perform the conversion. I’ve verified everything…

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[gmx-users] why not coordinates from cpt file

Post by gromacs queryHi allI have very simple query. While continuing simulations why we need to use*.gro (-c) with grompp as *.cpt (-t) has all the information (as checkedwith gmxcheck)?cpt file should suffice all the purposes. I tried using grompp providing -t*.cpt file but without -c *.gro file, it does…

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[lammps-users] moving graphene as rigid – LAMMPS Mailing List Mirror

Hello LAMMPS users, I am using windows 30 july 2021. units are real. I have a query regarding rigid command. I want to move graphene as a rigid body. For this I have created two groups. One group is fixedatoms (purple colored) and the second group is rigidcarbonatoms (grey color)….

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How to convert transcript-relative coordinates to genomic coordinates?

How to convert transcript-relative coordinates to genomic coordinates? 0 I have queried using Entrez Utilities (efetch: www.ncbi.nlm.nih.gov/books/NBK25499/) and obtained annotations for transcripts like the following: >Feature ref|NM_152486.3| 1 2557 gene gene SAMD11 gene_syn MRS gene_desc sterile alpha motif domain containing 11 db_xref GeneID:148398 db_xref HGNC:HGNC:28706 db_xref MIM:616765 How/what database should…

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taxonomy – Assign multiple taxids to a sequence when constructing a local BLAST database

I recently had a script fail due to poor handling of BLAST output. The BLAST -outfmt staxids field usually returns a single taxid, but occasionally it returns two or more taxids separated by a semicolon, such as 556514;701533. Fixing the script to handle this should be fairly straightforward. But the…

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Install CUDA on NVIDIA Jetson Nano

Hardware Pre-requisite Jetson Nano A 5V 4Ampere Charger 64GB SD card Software Preparing Your Raspberry Pi Flashing Jetson SD Card Image Unzip the SD card image Insert SD card into your system. Bring up Etcher tool and select the target SD card to which you want to flash the image….

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Convert list of Accession Numbers to Full Taxonomy

Using NCBI Entrez direct. $ esearch -db assembly -query “GCA_000005845” | elink -target taxonomy | efetch -format native -mode xml | grep ScientificName | awk -F “>|<” ‘BEGIN{ORS=”, “;}{print $3;}’ Escherichia coli str. K-12 substr. MG1655, cellular organisms, Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacterales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K-12, If…

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downloading RNA seq data

downloading RNA seq data 0 Hi friends I am using the following code to get the data from TCGA. I want to have only one allocate of each person then I will have unique patients ID. Is there any line of code that I should add to this to get…

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Bioconductor – GSE13015

DOI: 10.18129/B9.bioc.GSE13015     GEO accession data GSE13015_GPL6106 as a SummarizedExperiment Bioconductor version: Release (3.14) Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data…

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[lh3/minimap2] Memory leak when using Python and threads

The program align.py uses mappy to align reads in Python using multiple worker threads. After loading the index the memory usage jumps up quickly to >20Gb and then continues to climb steadily through 40Gb an beyond. This issue was first discovered in bonito and isolated to mappy. The data flow…

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Bwa on multiple processor

Hi Guys, When I am trying to run bwa mem on multiple processor, I am getting error as : > mpirun -np 16 bwa mem hg19-agilent.fasta R1.fastq R2.fastq | samtools sort -o aln.bam [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read…

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