Tag: GEO

genbank sequence format

HHS Vulnerability Disclosure, Help This document is an overview of the Entrez databases, with general information on If you are not sure that the “Save” option in your program will do this for you, use “Save As”, In Excel, select “Save As” from the File menu. optimizations to reduce memory…

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microarray analysis – gene upregulation/downregulation

microarray analysis – gene upregulation/downregulation 0 Hi guys, I have performed microarray differential expression analysis using the following R commands/script: library(“arrayQualityMetrics”) > library(GEOquery) > library(oligo) > library(Biobase) > library(affy) > library(“splitstackshape”) > library(“tidyr”) > library(dplyr) > celFiles <- list.celfiles() > affyRaw <- read.celfiles(celFiles) Platform design info loaded. Reading in :…

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How to convert single-cell RNAseq filename.mtx.gz to seurat object

How to convert single-cell RNAseq filename.mtx.gz to seurat object 0 Hi All, I need your great help with my public scRNAseq data obtained from GEO dataset analysis. For example, if I want to access this dataset (GSE118019) to convert it into Seurat object? There is no separate barcode, features, matrix…

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Bioconductor – RLHub (development version)

DOI: 10.18129/B9.bioc.RLHub     This is the development version of RLHub; for the stable release version, see RLHub. An ExperimentHub package for accessing processed RLSuite data sets Bioconductor version: Development (3.17) | RLHub provides a convenient interface to the processed data provided within RLSuite, a tool-chain for analyzing R-loop-mapping data…

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Nociceptor neurons affect cancer immunosurveillance

Secondary use of biopsies as research specimens The ten melanoma samples used in this study were collected by Sanford Health and classified by a board-certified pathologist. Their secondary use as research specimens (fully de-identified formalin-fixed, paraffin-embedded (FFPE) blocks) was approved under Sanford Health IRB protocol 640 (titled ‘Understanding and improving…

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howto:geometry_optimisation [CP2K Open Source Molecular Dynamics ] (2022)

Introduction This tutorial is designed to illustrate how to relax the structureof a system (without changing the cell dimensions) using CP2K. Weuse the relaxation of a water (H\(_2\)O) molecule as an example. The example files are contained in geometry_optimisation.tgz that comes with this tutorial. The calculation was carried out with…

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Bioinformatic Analyst job at Tellus Solutions in Remote

Job description Tellus Solutions is in partnership with a committed biopharmaceutical company in North Chicago focused on providing innovative therapies. Your technical expertise as a Bioinformatics analyst in the area of using R to do basic data analysis (processing, plotting), RNA-Seq alignment experience will contribute to our client’s innovative therapies…

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Microarray DEG scatterplot

Hi, I have found that my selected gene, probe I.D 201667_at is differentially expressed between WDLPS and DDLPS tumour tissue samples after performing microarray DEG analysis. Instead of just a p value in a table format: Probe I.D “201667_at” logFC 10.8205874181535 AveExpr 10.6925705768407 t 82.8808890739766 P.Value 3.10189446528995e-88 adj.P Val 3.10189446528995e-88…

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How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger)

How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger) 0 Hello all. I am trying to pre-process some single cell RNA and ADT (Totalseq-C) data from an GEO SRA, but having some issues getting separate fastq’s for the “CITE-seq” (ADT)…

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Job – Principal Biostistician/Bioinformatics job at Kenya Medical Research

Vacancy title: Principal Biostistician/Bioinformatics [ Type: FULL TIME , Industry: Research , Category: Research ] Jobs at: Kenya Medical Research – KEMRI Deadline of this Job: 06 October 2022   Duty Station: Within Kenya , Kisumu , East Africa SummaryDate Posted: Tuesday, September 20, 2022 , Base Salary: Not Disclosed…

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A global dataset of microbial community in ticks from metagenome study

Data collection The study was performed according to the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement20. To attain an exhaustive review of the published literature on the microbiome diversity by NGS in field-collected ticks, a literature search was conducted on Chinese and English databases using a set…

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Global Gene Therapy R&D Market Worth US$ 22,685.70 million by 2031: Visiongain Reports Ltd

Visiongain Reports Ltd Global Gene Therapy R&D Market Forecast 2021-2031: – Market Segment by Disease {Cancer, Rare Diseases (Oncologic, Non-Oncologic), Cardiovascular Diseases, Ophthalmic Diseases, Hematology, Neurological, Diabetes Mellitus, Other Diseases}, Vector {Viral (Retrovirus, Adenovirus, AAV, Lentivirus, Others), Non-Viral (Naked DNA, Gene Gun, Electroporation, Lipofection)}, Techniques (Gene Augmentation Therapy, Gene Replacement…

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Bioinformatics Analysis of the Key Genes and Pathways in Multiple Myel

Introduction Multiple myeloma is a B-cell malignancy characterized by the malignant proliferation of clonal plasma cells in bone marrow,1 It is the second most common hematological malignancy after lymphoma.2 The age-standardised rate (ASR) of multiple myeloma incidence was 1·78 (95% UI 1·69-1·87) per 100 000 people globally and mortality was…

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Acute phase of ischemia-reperfusion in rats

Introduction Stroke is one of the leading causes of death and disability worldwide, which causes substantial economic and social burdens.1 Ischemic stroke is caused by insufficient blood and oxygen supply to the brain,2 accounting for about 85% of the casualties of stroke patients.3 The concept of treatment for ischemic injury…

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Live-seq enables temporal transcriptomic recording of single cells

Biological materials RAW264.7, 293T and HeLa cells were obtained from ATCC. RAW264.7 cells with Tnf-mCherry reporter and relA-GFP fusion protein (RAW-G9 clone) were kindly provided by I.D.C. Fraser (National Institutes of Health). The IBA cell line derived from the stromal vascular fraction of interscapular brown adipose tissue of young male…

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Scientist I, Bioinformatics job at Vir Biotechnology in United States – 53516780

Vir Biotechnology is a commercial-stage immunology company focused on combining immunologic insights with cutting-edge technologies to treat and prevent serious infectious diseases. Vir has assembled four technology platforms that are designed to stimulate and enhance the immune system by exploiting critical observations of natural immune processes. Its current development pipeline…

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Immune Infiltration and N(6)-Methyladenosine ncRNA Isoform Detection in Acute Lung Injury

Acute lung injury (ALI) is a severe form of sepsis that is associated with a high rate of morbidity and death in critically ill individuals. The emergence of ALI is the result of several factors at work. Case mortality rates might range from 40% to 70%. Researchers have discovered that…

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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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exact counts tables for limma voom guide

exact counts tables for limma voom guide 1 Is there a way to download the exact counts table associated with the limma voom guide? specifically for the tutorial in chapter 15 of the limma voom guide (GSE64099). I would like to to run through the commands and recreate the plots…

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A Standardized, Specification-Driven API Lifecycle

Transcript Lane: I’d like to share with you a high level view of why API specifications matter. How OpenAPI, AsyncAPI, JSON Schema and others are helping us standardize and deliver API lifecycle in a way that the machines understand. Also, allows us humans to better communicate, collaborate, and move forward…

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Roles of circRNAs | CMAR

Introduction Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, with an increasing global incidence, and a leading cause of cancer-related mortality.1 Although hepatitis B and C virus infections, cirrhosis, alcohol intake, and non-alcoholic fatty liver disease (NAFLD) are the main risk factors contributing to HCC.1,2 Approximately…

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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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MND1 Expression as a Predictor of Breast Cancer Survival

Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…

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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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Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

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Analysis of circRNA-miRNA-mRNA Regulatory Network in Peripheral Blood of Radiation Workers

The health of radiation workers has always been our focus. Epidemiological investigation shows that long-term exposure to low-dose ionizing radiation can affect human health, especially cancer and cardiovascular disease, and there are many studies on it. However, up to now, there have been few reports on the research of blood…

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GEO Browser – GEO – NCBI

Filter Mus musculus TSV Brian P. Hermann GSE109033 10x Genonics Drop-seq single-cell RNA-seq of isolated Adult ID4-EGFP mouse spermatogonia, spermatocytes, spermatids & steady-state spermatogenic cells Expression profiling by high throughput sequencing Mus musculus 8 MTX TSV SRA Run Selector Brian P. Hermann Nov 06, 2018 GSE109037 10x Genomics Drop-seq single-cell…

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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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Multi-purpose GNSS Receiver Market 2022 with Top Countries Data Analysis by Industry Trends, Size, Share, Company Overview, Growth, Development and Forecast by 2028

The recently published Multi-purpose GNSS Receiver market report sheds lights on industry segments, competitive scenario, geographical expansion, and important facets like revenue, production, consumption, and Covid-19 footprint. The latest research report on the Multi-purpose GNSS Receiver market encompasses an in-depth assessment of this industry, and a creditable brief of its…

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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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Construction of a circRNA-Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection

Background: Aortic dissection (AD) is a rare and lethal disorder with its genetic basis remains largely unknown. Many studies have confirmed that circRNAs play important roles in various physiological and pathological processes. However, the roles of circRNAs in AD are still unclear and need further investigation. The present study aimed…

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A hypoxia-related signature in lung squamous cell carcinoma

Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…

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bioconductor – Unable to install GEOquery

I just installed Bioconductor in RStudio 4.1.1: if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) I am currently trying to install GEOquery package from Bioconductor but it is throwing error messages and I don’t know what the problem is or how to fix it: BiocManager::install(“GEOquery”) Error Message: ‘getOption(“repos”)’ replaces Bioconductor standard repositories,…

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Bioinformatics analysis identifies widely expressed genes

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

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Genetic characteristics involving the PD-1/PD-L1/L2 and CD73/A2aR axes and the immunosuppressive microenvironment in DLBCL

Key messages What is already known on this topic Targeting immunosuppressive pathways have emerged as promising strategies for cancer treatment. The genetic characteristics of PD-1/PD-L1/L2 (programmed cell death protein 1/programmed cell death ligand 1/ligand 2) and CD73/A2aR (A2a adenosine receptor) and the effect of these two signalings on dysfunctional CD8+…

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Need RNAseq dataset with many samples for machine learning project

Need RNAseq dataset with many samples for machine learning project 0 I’m looking to train a machine learning model on Alzheimer’s disease transcriptome versus non-AD transcriptome. I want to train the model to differentiate between the 2 so I can then learn which genes are most important for distinguishing. I…

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Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis

Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS  Google Scholar  Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…

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Thymidine Kinase 1 Drives Skin Cutaneous Melanoma Malignant Progression and Metabolic Reprogramming

Background: Thymidine kinase 1 (TK1) is a cell cycle-dependent kinase that catalyzes the addition of a gamma-phosphate group to thymidine. The protumorigenic role of TK1 has been reported in various malignancies. However, the role of TK1 in skin cutaneous melanoma (SKCM) remains unclear. This study aimed to explore the molecular…

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Analysis of differential gene expression of bulk RNA-seq data using “DESeq2” in RStudio. – Yale Library Study Spaces Scheduling

RNA-Seq is a high-throughput sequencing method used for unbiased detection and quantification of messenger RNA molecules, allowing the identification of genes and pathways underlying normal and pathological conditions. RNA-seq sequencing services are increasingly affordable which has led to the proliferation of published data available in public repositories accessible for everyone’s…

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Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape

Karesh, W. B. et al. Ecology of zoonoses: natural and unnatural histories. Lancet 380, 1936–1945 (2012). PubMed  PubMed Central  Google Scholar  Wolfe, N. D., Dunavan, C. P. & Diamond, J. Origins of major human infectious diseases. Nature 447, 279–283 (2007). CAS  PubMed  PubMed Central  Google Scholar  Allen, T. et al….

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Job Research Associate (PostDoc) in Bioinformatics (f/m/x) – Helmholtz-Zentrum Potsdam – Deutsches GeoForschungsZentrum GFZ

This vacancy is published within the academics.com initiative #ResearchersAtRisk. In the case of applications of researchers in risk, the special biographical circumstances are taken into account. The Helmholtz Centre Potsdam – GFZ German Research Centre for Geosciences is the national centre for geosphere research. As a member of the Helmholtz…

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Processing Illumina HumanHT-12 V4.0 data without detection p-values

Processing Illumina HumanHT-12 V4.0 data without detection p-values 1 Hello, I want to pre-process GSE17048 dataset from GEO. I followed the steps provided by Kevin in this post but I realized that neqc from limma requires the detection p-values of each probe for normalizing the data. I wanted to know…

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Transcriptional kinetics and molecular functions of long noncoding RNAs

Ethical compliance The research carried out in this study has been approved by the Swedish Board of Agriculture, Jordbruksverket: N343/12. Cell culture Mouse primary fibroblasts were derived from adult (>10 weeks old) CAST/EiJ × C57BL/6J or C57BL/6J × CAST/EiJ mice by skinning, mincing and culturing tail explants (for at least 10 d) in DMEM high…

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Identification of Hub Genes Associated with COPD Through Integrated Bi

Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…

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Modeling injury and repair in kidney organoids reveals that homologous recombination governs tubular intrinsic repair

Submission history Received: 28 May 2021 Accepted: 14 January 2022 Acknowledgments We thank J. V. Bonventre, J. A. Lewis, and E. P. Rhee for institutional support; S. J. Hill for insightful discussion and sharing antibodies; Y. Yoda for cell culture; L. Racusen of Johns Hopkins University for the HKC-8 cell…

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Weird movement of Pt (fcc 111) layers with one OH radical on top

Dear CP2K users, I am performing geometry optimizations for Pt slab (fcc111) with one hydroxyl (OH) radical on top. First, the cell optimization of bulk Pt (fcc111) is performed and successfully converged (Pt_cellopt.xyz).  However, when I put one OH radical on Pt 111 to perform geometry optimization, I observed a…

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Exosomal microRNA-618 derived from mesenchymal stem cells attenuate the progression of hepatic fibrosis by targeting Smad4

Introduction Hepatic fibrosis (HF) is a pathological phenomenon produced in the process of long-term damage and repair in the liver [1,2]. During the formation of HF, hepatocytes are damaged by various factors, such as chronic liver disease, and excessive intake of alcohol, and secrete a variety of cytokines [3]. Subsequently,…

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Comprehensive bioinformatics analysis reveals the hub genes and pathways associated with multiple myeloma

This article was originally published here Hematology. 2022 Dec;27(1):280-292. doi: 10.1080/16078454.2022.2040123. ABSTRACT PURPOSE: While the prognosis of multiple myeloma (MM) has significantly improved over the last decade because of new treatment options, it remains incurable. Aetiological explanations and biological targets based on genomics may provide additional help for rational disease…

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Validation of hub genes in acute pancreatitis

Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…

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CAMBREEN-WEEDER-BIOMOBY 3geonames

CAMBREEN-WEEDER-BIOMOBY Pick a Random location anywhere API Pick a Random location proximal to Land 78.489530, 17.759360, 0 Source Code Perl5 Geo::Code::XYZ README Reverse Geocode.xyz Near Philippbreen Svalbard Spitsbergen SJ Elevation: 632 metres TimeZone: Arctic/Longyearbyen Points of Interest around 78.489530,17.759360 Results from Reverse Geocoder Lite api.3geonames.org/78.489530,17.759360 Geocode.xyz/78.489530,17.759360 N6D2H5UWRW CAMBREEN-TKH5B0 🇸🇯 Nearby…

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Fatty infiltration after rotator cuff tear

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

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Top tech innovations we may see in 2022

Data science, artificial intelligence and analytics are disrupting the technological landscape as we know it. The pandemic has only accelerated this growth, which is just the start. One of the obvious paths ahead is the convergence of these various technologies to create more advanced solutions and applications.  The Ark Big…

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Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition

INTRODUCTION Mammalian life starts with the fusion of two terminally differentiated gametes, sperm and oocyte, resulting in a totipotent zygote. After going through preimplantation development, the zygote reaches blastocyst before implantation. The two most important events taking place during preimplantation development are zygotic genome activation (ZGA) and the first cell…

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Identification of a four-gene signature & PTC.

Introduction Thyroid carcinoma (THCA) is the most common type of endocrine malignancy and its incidence is increasing.1 Based on its histopathological characteristics, thyroid carcinoma can be classified into multiple subtypes, such as papillary thyroid carcinoma (PTC), follicular thyroid carcinoma, and anaplastic thyroid carcinoma.2 PTC is the most common subtype of…

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Immune microenvironment-related gene mapping predicts immunochemotherapy response and prognosis in diffuse large B-cell lymphoma

doi: 10.1007/s12032-021-01642-3. Affiliations Expand Affiliations 1 Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. 2 Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China. 3 Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China. 4 Department of Blood Transfusion, Nanfang Hospital, Southern…

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Novel diagnostic biomarkers for keloid based on GEO database

Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…

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[BioC] problem with GEOquery

Hi to everybody, i have a little problem with GEOquery .i when I’m trying to download the GSE2841 dataset I encounter the gse <- getGEO(“GSE2841”) try with URL‘ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2841_family.soft.gz’Error in downloading the.file(myurl, destfile, mode = mode) :impossible to open URL‘ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2841_family.soft.gz'&#8221; why???????????? Please help me Best regards Dr Alberto GoldoniMedical Genetics UnitS….

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The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

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ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes | BMC Bioinformatics

1. Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, et al. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016;17:66. Article  Google Scholar  2. Minio A, Lin J, Gaut BS, Cantu D. How single…

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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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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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Identification of differentially expressed genes in AF

Defeng Pan,1,&ast; Yufei Zhou,2,&ast; Shengjue Xiao,1,&ast; Yue Hu,3,&ast; Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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Getting peak heights from TF chIP-seq data (wig file)

Getting peak heights from TF chIP-seq data (wig file) 1 Hello everyone, I have TF ChIP seq data from NCBI GEO in wig format. I converted wig to bedgraph and then used MACS peak caller to get bed narrowpeak files.I further uploaded file on genome browser to get graphical map…

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Crosstalk between Venous Thromboembolism and Periodontal Diseases: A Bioinformatics Analysis

This article was originally published here Dis Markers. 2021 Dec 10;2021:1776567. doi: 10.1155/2021/1776567. eCollection 2021. ABSTRACT BACKGROUND: This current study applied bioinformatics analysis to reveal the crosstalk between venous thromboembolism (VTE) and periodontitis, as well as the potential role of immune-related genes in this context. METHODS: Expression data were downloaded…

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Adrenal aldosterone-producing adenoma | IJGM

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

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Problem for analysing GSEA and ORA

Problem for analysing GSEA and ORA 0 I analysed two different GEO dataset individually and found DEG for each dataset .After that I compare the two dataset DEG and found some common DEG.Now i want to analyse GSEA and ORA for that common DEG.As far i know for analysing GSEA…

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Prognosis Biomarkers via WGCNA in HCC

Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…

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Intersecting Roadmap’s Histone ChIP-seq data using BedTools?!?!??!

Intersecting Roadmap’s Histone ChIP-seq data using BedTools?!?!??! 0 Hi all, I want to prioritise my list of 112 SNPs by looking at those that lie within open chromatin regions and/or active promoter/enhancer histone marks In order to do that I have downloaded several Histone modification ChIP-seq data from Roadmap epigenomics…

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How to convert cloupe files to mtx

How to convert cloupe files to mtx 1 I have 2 cloupe files from a project on GEO. I need to reprocess this data but cannot find a way to extract the gene expression table from the cloupe files. I tried Loupe Browser from cell ranger but this only allows…

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Identification of Hub Genes in Patients with Alzheimer Disease and Obs

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

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Identification of circRNA-miRNA-mRNA Regulatory Network and Autophagy Interaction Network in Atrial Fibrillation Based on Bioinformatics Analysis

Background: Circular RNA (circRNA) has been receiving increased attention in the research of atrial fibrillation (AF). Our study aims to find potential circRNAs and identify the circRNA-miRNA-mRNA regulatory network in AF based on bioinformatics analysis. Methods: GSE129409 was retrieved from the Gene Expression Omnibus (GEO) database, and we used R…

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Dropseq, GSE124872 and structure of the reads in the FastQ files

Hello I am confused by the structure of the reads in a FastQ File I downloaded via GEO. The data is stored in GEO GSE124872, GSM3557675. According the SRA Run Selector, there is one FastQ file per sample, but the paper* and SRA mention that the data is paired end….

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Comment: Importing GEO dataset

my sessionInfo() output is R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.2.2 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.1.1 tools_4.1.1 Read more here: Source…

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Potenial biomarker in Crohn’s diease via bioinformatics

Introduction Crohn’s disease (CD) and ulcerative colitis are chronic inflammatory disorders of the gastrointestinal tract, with symptoms evolving in a relapsing and remitting manner that comprise the term inflammatory bowel disease (IBD).1 CD is characterized by the involvement of all parts of the intestine, the most common being the terminal…

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What is a count matrix for input into Seurat supposed to look like?

Hello, I hope you are safe and well. Could someone share what a count matrix for input into Seurat is supposed to look like? I have count matrices however they each cells count matrix is in a separate file. This is the data I want to analyze in Monocle 3:…

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Genome Size Estimation with Jellyfish and Genome Scope is Unexpectedly Small

I used jellyfish to count kmers and the obtained histograms were analyzed using Genome scope (qb.cshl.edu/genomescope/) in order to estimate effective genome size. However the resulting bp estimation of 61,351 bps is unexpectedly small for human data. The paired-end data was obtained from a Chip-seq experiment on Geo (GSE72141). Additionally,…

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The Construction and Comprehensive Analysis of a ceRNA Immunoregulator

1Department of Cardiology, Xiangtan Central Hospital, Xiangtan, Hunan, People’s Republic of China; 2Department of Cardiology, Guangxi Cardiovascular Institute, The First Affiliated Hospital of Guangxi Medical University, Guangxi, People’s Republic of China; 3Department of Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, Hunan, People’s Republic of China Correspondence: Yiqian ZengDepartment of Critical…

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Comprehensive analysis of ceRNA networks to determine genes related to prognosis, overall survival, and immune infiltration in clear cell renal carcinoma

Comput Biol Med. 2021 Nov 20:105043. doi: 10.1016/j.compbiomed.2021.105043. Online ahead of print. ABSTRACT BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is one of the common subtypes of kidney cancer. Circular RNAs (circRNAs) act as competing endogenous RNAs (ceRNAs) to affect the expression of microRNAs (miRNAs), and hence the expression of…

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Collabera Inc. hiring Bioinformatics Analyst in North Chicago, Illinois, United States

Job Description We have an exciting contract opportunity for a Bioinformatics Analyst to perform bulk differential gene. Ideally microarray and RNA-seq and enrichment analysis in the R programing language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential gene limma/variance Parition…

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Importing GEO dataset

I need to import data GSE76124 in R studio the command I used is library(GEOquery) my_id <- "GSE76124" gse <- getGEO(my_id) the output and warning I'm getting is : Found 1 file(s) GSE76124_series_matrix.txt.gz trying URL 'ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76124/matrix/GSE76124_series_matrix.txt.gz&#039; Content type 'application/x-gzip' length 58695125 bytes (56.0 MB) ================================================== downloaded 56.0 MB Error: The…

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Bioinformatics Scientist at Infectious Disease Institute

IDI seeks to hire a Bioinformatics Scientist (BS) for the centre. The BS will be a fulltime staff who is familiar with the application of computational and biotechnology capabilities to biomedical and public health problems like genetics, clinical and medical research, as well as other data intensive analyses. By coordinating…

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Index of /~psgendb/doc/local/biopython-1.64.old/Tests/output

Name Last modified Size Description Parent Directory   –   test_AlignIO 2014-05-29 05:23 31K   test_AlignIO_FastaIO 2014-05-29 05:23 60K   test_ClustalOmega_tool 2014-05-29 05:23 1.2K   test_Clustalw 2014-05-29 05:23 5.8K   test_Clustalw_tool 2014-05-29 05:23 1.3K   test_CodonTable 2014-05-29 05:23 21   test_CodonUsage 2014-05-29 05:23 784   test_DocSQL 2014-05-29 05:23 42  …

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Most useful public genomic/genetic databases/tools/applications

Forum:Most useful public genomic/genetic databases/tools/applications 1 Hi guys, I am looking for suggestions/recommendations from the research community regarding public databases that are most commonly used by researchers in their analysis. These could be the open access data or controlled access. Also, what are some of the applications used most commonly…

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Bioconductor – GSE159526

DOI: 10.18129/B9.bioc.GSE159526     Placental cell DNA methylation data from GEO accession GSE159526 Bioconductor version: Release (3.14) 19 term and 9 first trimester placental chorionic villi and matched cell-sorted samples ran on Illumina HumanMethylationEPIC DNA methylation microarrays. This data was made available on GEO accession [GSE159526](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159526). Both the raw and…

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Bioinformatics analysis pinpoints the pathways involved in intestinal SARS/CoV-2 infection

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is a positive-strand RNA virus, which appears spherical under a transmission electron microscope. Many studies have shown that SARS-CoV-2 infects host cells via the interaction between the viral spike protein and the host receptor, angiotensin-converting enzyme II (ACE2). SARS-CoV-2 can spread through…

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WGCNA Analysis Identifies Polycystic Ovary Syndrome-Associated Circula

Introduction Polycystic ovary syndrome (PCOS) is a common endocrine metabolic disorder in women of childbearing age.1 PCOS patients are typically characterized by androgen excess, polycystic ovaries and anovulation, and are often accompanied by insulin resistance and obesity.2 Consequently, patients with this syndrome not only suffer from infertility,3 but also have…

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Bioconductor – tuberculosis

DOI: 10.18129/B9.bioc.tuberculosis     Tuberculosis Gene Expression Data for Machine Learning Bioconductor version: Release (3.14) The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been…

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PyTorch implementation of our ICCV 2021 paper Intrinsic-Extrinsic Preserved GANs for Unsupervised 3D Pose Transfer.

This is the PyTorch implementation of our ICCV 2021 paper Intrinsic-Extrinsic Preserved GANs for Unsupervised 3D Pose Transfer. Haoyu Chen, Hao Tang, Henglin Shi, Wei Peng, Nicu Sebe, Guoying Zhao. Citation If you use our code or paper, please consider citing: @inproceedings{chen2021IEPGAN, title={Intrinsic-Extrinsic Preserved GANs for Unsupervised 3D Pose Transfer}, …

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Index of /~psgendb/local/biopython-1.64.old/Bio

Name Last modified Size Description Parent Directory   –   Affy/ 2014-05-29 05:25 –   Align/ 2014-06-11 10:27 –   AlignIO/ 2014-06-11 10:27 –   Alphabet/ 2014-06-11 10:27 –   Application/ 2014-05-29 05:25 –   Blast/ 2014-05-29 05:25 –   CAPS/ 2014-05-29 05:25 –   Cluster/ 2014-05-29 05:25 –  …

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circRNA-miRNA-mRNA regulatory network in atrial fibrillation

Introduction Atrial fibrillation (AF) is the most common type of arrhythmia in clinical practice, with global prevalence continuing to increase primarily with age.1 In China, 6.5 persons out of every thousand suffer from AF, and there are about 3.9 million patients with AF who are over 60 years old, but…

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Differential gene expression analysis on microarray dataset with files from two chips

Hello all, I’m used to analyzing mostly RNAseq data, microarray is a bit new to me. I’m trying to analyze data from www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47183 in R. When I try to read in the .CEL files using read.celfiles() from the oligo package, it informs me that the CEL files are not of…

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Genes and Pathways Involved in Postmenopausal Osteoporosis

Introduction Many postmenopausal women suffer from postmenopausal osteoporosis (PMO). A survey of 3247 Italian postmenopausal women found that according to bone mineral density (BMD) diagnostic criteria, the prevalence of osteoporosis was 36.6%.1 PMO patients may suffer from chronic pain and fractures, and as a result their quality of life is…

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Multiple stages of evolutionary change in anthrax toxin receptor expression in humans

Human research participants We have complied with all relevant ethical regulations and informed consent was obtained from all participants. This work was approved by the Cornell University IRB under protocol 1506005662. Animal research This work was approved by the Cornell University IACUC under protocol 2009-0044. Welfare and handling of all…

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Not able to show data on choropleth map with ggplot2 – R Markdown

Hi everyone, I am working on some data visualisations for a project. I have very limited experience with R so any help will be greatly appreciated. I have run the code below. I have gotten a map but no colours and Co2 Emission data for the countries. Co2_Country_Graph4=plot_geo(Co2Country3,locationmode =”country”,frame= ~Year)%>%add_trace(location…

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sequencing – Plotting QC output for scRNA data analysis using Seurat R and accessing Seurat object data

I am new to R, and want to analyse some public scRNA seq data published in Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP et al. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell 2018 Nov 1;175 (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120575). I have tried to follow the online…

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Sending Fasta files : bioinformatics

What is the source of your fasta file? If it’s your personal data from sequencing I would not give it out without ensuring they are keeping anonymity and proper ethical considerations, like who else will this file be shared with and how. Many publications have Geo datasets or SRA archives…

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How to load GEO datasets for analysis using Scvi tools/Scanpy? : bioinformatics

I am super new to bioinformatics and omics studies. I am currently trying to analyse single cell RNA seq data using Scanpy and Scvi, and I am trying it out with datasets on GEO. They look a little different than the ones that were used in the tutorials. It seems…

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Error using getGEO – error reading from the connection

Error using getGEO – error reading from the connection 0 Hi, I’ve been trying to open GEO data in R studio. So far I have the following code, copied from a tutorial: #tutorial for analysing data from GEO library(GEOquery) my_id <- “GSE33126” gse <- getGEO(my_id) However, I get the following…

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Error using getGEO

Hi, I’ve been trying to open GEO data in R studio. So far I have the following code, copied from a tutorial: library(GEOquery) my_id <- “GSE33126” gse <- getGEO(my_id) However, I get the following error when running this code: Found 1 file(s) GSE33126_series_matrix.txt.gz trying URL ‘ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33126/matrix/GSE33126_series_matrix.txt.gz‘ Content type ‘application/x-gzip’ length…

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