Tag: ICA
How the UK is setting new standards for genomic research and better health care
Last week, UK Biobank released the sequence analysis of half a million samples to approved researchers across academia, industry, charitable organizations, and government. Experts believe this milestone will greatly aid scientists in drug discovery and other biomedical developments. “This is a fundamentally important project in terms of enabling access to…
Validation of expressions given input sections – CWL Questions
mvdbeek November 10, 2023, 9:13am 1 Is it possible to catch expressions that access (potentially) undefined variables before runtime ? Take as an example the following diff as applied to github.com/common-workflow-library/bio-cwl-tools/blob/91c42fb809ce18eafe16155cca0abf362270c0fe/fastp/fastp.cwl: diff –git a/fastp/fastp.cwl b/fastp/fastp.cwl index 575c91f..b6be4eb 100755 — a/fastp/fastp.cwl +++ b/fastp/fastp.cwl @@ -19,7 +19,7 @@ baseCommand: fastp arguments: -…
Illumina hiring Bioinformatics Software Development in Great Abington, England, United Kingdom
What if the work you did every day could impact the lives of people you know? Or all of humanity?At Illumina, we are expanding access to genomic technology to realize health equity for billions of people around the world. Our efforts enable life-changing discoveries that are transforming human health through…
Batch correction in DESeq2 – limited impact for unsupervised downstream analyses
Hello, I need to normalize gene expression (RNASeq) data to perform downstream analyses on it: unsupervised deconvolution using ICA pathway quantification using decoupleR. I want to see which pathways are important in my cohort and if some pathways are specific to subgroups of clinical features (histology, stage, …). Actually, to…
Field Bioinformatics Scientist job in Bengaluru
Bengaluru, India Illumina Full time What if the work you did every day could impact the lives of people you know? Or all of humanity?At Illumina, we are expanding access to genomic technology to realize health equity for billions of people around the…
R studio freezes when monocle3 is installed – RStudio IDE
Hi, R studio server freezes and the .Rproj.user and .Rhistory files must be deleted to connect to an already running session. This behaviour is only resolved by uninstalling monocle3 and comes back when I re-install monocle3. I tried the development and beta branch of Monocle3. I had the same issue…
Field Bioinformatics Scientist job in Bangalore
Bangalore, India Illumina Full time What if the work you did every day could impact the lives of people you know? Or all of humanity?At Illumina, we are expanding access to genomic technology to realize health equity for billions of people around the…
Leveraging SageMath and ChatGPT for (orthogonal) diagonalization and singular value decomposition
[1] S. Andrilli, D. Hecker, Elementary Linear Algebra, Sixth edition, Academic Press, Cambridge, Massachusetts, US, 2022. doi.org/10.1016/C2019-0-03227-X [2] H. Anton, C. Rorres, Elementary Linear Algebra: Applications Version, 12th edition, John Wiley & Sons, New York, US, 2013. …
Alliance for Genomic Discovery FAQs | VUMC Reporter
Alliance for Genomic Discovery (AGD) FAQs – July 2023 – What is Nashville Biosciences? Nashville Biosciences (“NashBio”) is a wholly owned for-profit subsidiary of VUMC, launched in 2018 (www.nashville.bio/). Read the news: The Alliance for Genomic Discovery announces founding biopharma members: AbbVie, Amgen, AstraZeneca, Bayer and Merck Why was…
Altered Signaling and Desensitization Responses in PTH1R Mutants Associated with Eiken Syndrome
Plasma membrane expression of WT and mutant PTH1Rs The positions in the PTH1R of the three studied mutations of Eiken syndrome, E35K, Y134S and R485X, as well as the H223R mutation of JMC are shown in Fig. 1a and b. Cell surface expression of the receptors in transiently transfected HEK293-derived Gs22a…
Flora diversity survey and establishment of a plant DNA barcode database of Lomas ecosystems in Peru
Dillon, M. O., Nakazawa, M. & González, S. L. The Lomas formations of coastal Peru: Composition and biogeographic history. Vol. 43 1–9 (Botany New Series, 2003). Chávez, R. O. et al. GIMMS NDVI time series reveal the extent, duration, and intensity of “blooming desert” events in the hyper-arid Atacama Desert,…
lfcshrink error DESeq2
Hello! I’m having problems with lfcShrink in my DESeq2 workflow. I’m trying to do a differential expression analysis (with only one comparison term: “MULTIseq_ID_call2”) on my single-cell data. However when I do lfcShrink I get an error that I cannot interpret. Can you help me? dds <- DESeq(dds, test =…
Mutation Detection Kits in Genome Editing Market to Reach at
Mutation Detection Kits in Genome Editing Market Mutation Detection Kits In Genome Editing Market: Size, Share & Trends Analysis Report By Technology (CRISPR/Cas9, TALENs/MegaTALs, ZFN, Mega nucleases), By End-use, and Region (North America, Europe, Asia-Pacific, Middle East and Africa and South America) Get a FREE Sample Copy of this Report…
Running accurate, comprehensive, and efficient genomics workflows on AWS using Illumina DRAGEN v4.0
Introduction The reduced cost of DNA sequencing technology has led to an exponential growth of raw sequencing data. To keep pace with this development, secondary analysis tools that can provide fast and accurate results in a cost-effective manner are needed to extract actionable genomic insights. Illumina’s DRAGENTM (Dynamic Read Analysis for GENomics) addresses…
Unable to install clusterProfiler on Mac M1
Hi, I failed to install clusterProfiler on Mac M1. May I ask the solution >BiocManager::install(“clusterProfiler”) Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.3 (2022-03-10) Installing package(s) ‘clusterProfiler’ also installing the dependencies ‘fgsea’, ‘DOSE’, ‘enrichplot’, ‘GOSemSim’ Warning: unable to access index for repository bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL ‘https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES’ Warning: unable to access…
The Global Bioinformatics Market size is expected to reach $19.9 billion by 2028, rising at a market growth of 12.5% CAGR during the forecast period
ReportLinker In order to serve several fields of scientific study, including biomedicine, bioinformatics—a mix of biology and information technology—links biological data with methods for information storage, dissemination, and analysis. New York, Jan. 27, 2023 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “Global Bioinformatics Market Size, Share &…
lazy loading failed, unable to load shared object rtracklayer.so
Hello! I am working on analyzing a dataset I created with the 10x Chromium Single Cell Multiome kit. In order to add gene annotation to the ATAC data, I am trying to install and use the “EnsDb.Mmusculus.v79” and “BSgenome.Mmusculus.UCSC.mm10” packages with bioconductor. The same ERROR has come up repeatedly whenever…
Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline
Software Figure preparation: CorelDRAW x8 (Corel); Bioinformatic analyses: R v 4.0.3 (R Foundation for Statistical Computing). Computational resources Analyses were run on a desktop computer with an Intel Core i9-10900L CPU (3.70 GHz, 10 cores, 20 threads) with 120 GB RAM running Windows 10 Pro (v21H2). Data preprocessing scRNA-seq data sets…
Bioconductor Package Installation
When I try to install the gtf for hg38 BiocManager::install(“TxDb.Hsapiens.UCSC.hg38.knownGene”) I get the following error: ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ Error in readRDS(dest) : error reading from connection Per stackoverflow.com/questions/67455984/getoptionrepos-replaces-bioconductor-standard-repositories-see-reposito I…
SCIRP Open Access
Add your e-mail address to receive free newsletters from SCIRP. Select Journal AA AAD AAR AASoci AAST ABB ABC ABCR ACES ACS ACT AD ADR AE AER AHS AID AiM AIT AJAC AJC AJCC AJCM AJIBM AJMB AJOR AJPS ALAMT ALC ALS AM AMI AMPC ANP APD APE APM ARS ARSci AS ASM BLR CC CE CellBio ChnStd CM CMB CN CRCM CS CSTA CUS CWEEE Detection EMAE ENG EPE ETSN FMAR FNS GEP GIS GM Graphene GSC Health IB ICA IIM IJAA IJAMSC IJCCE IJCM IJCNS IJG IJIDS IJIS IJMNTA IJMPCERO IJNM IJOC IJOHNS InfraMatics JACEN JAMP JASMI JBBS JBCPR JBiSE JBM JBNB JBPC JCC JCDSA JCPT JCT JDAIP JDM JEAS JECTC JEMAA JEP JFCMV JFRM JGIS JHEPGC JHRSS JIBTVA JILSA JIS JMF JMGBND JMMCE JMP JPEE JQIS JSBS JSEA JSEMAT JSIP JSS JSSM JST JTR JTST JTTs JWARP LCE MC ME MI MME MNSMS MPS MR MRC MRI MSA MSCE NJGC NM NR NS OALib OALibJ ODEM OJA OJAB OJAcct OJAnes OJAP OJApo OJAppS OJAPr OJAS OJBD OJBIPHY OJBM OJC OJCB OJCD OJCE OJCM OJD OJDer OJDM OJE OJEE OJEM OJEMD OJEpi OJER OJF OJFD OJG OJGas OJGen OJI OJIC OJIM OJINM OJL OJM OJMC OJMetal OJMH OJMI OJMIP OJML OJMM OJMN OJMP OJMS OJMSi OJN OJNeph OJO OJOG OJOGas OJOp OJOph OJOPM OJOTS OJPathology OJPC OJPChem OJPed OJPM OJPP OJPS OJPsych OJRA OJRad OJRD OJRM OJS OJSS OJSST OJST OJSTA OJTR OJTS OJU OJVM OPJ POS PP PST PSYCH SAR SCD SGRE SM SN SNL Soft SS TEL TI UOAJ VP WET WJA WJCD WJCMP WJCS WJET WJM WJNS WJNSE WJNST WJV WSN YM Read more here: Source link
Senior Bioinformatics Support Scientist | Illumina
Why Us Illumina are growing at pace, and we are looking for the best customer focused Bioinformatics Support Scientist to join our mission, to improve human health by unlocking the power of the genome. By joining Illumina as a Bioinformatics Support Scientist in our EMEA Head Office, Cambridge UK, you will help support…
spots not filling the whole tissue image
Issue with Seurat SpatialPlot: spots not filling the whole tissue image 0 In Seurat, SpatialPlot generates a plot with an enlarged/expanded image of tissue section as compared to the original spot image. This seems to happen on the relatively small image with a number of spots around 500. I ‘d…
ICA – Reconstruction Errors
ICA – Reconstruction Errors 0 Hello people! I am completely new to the topic of ML and Omics and at all in the bioinformatics field. To gather some knowledge I started to work through a book I found on the internet and there is the following task: “Produce a 10-component…
