Tag: gtex

1. Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). CAS  PubMed  PubMed Central  Google Scholar  2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed…

Standard name KINNEY_DNMT1_METHYLATION_TARGETS Systematic name M2508 Brief description Hypomethylated genes in prostate tissue from mice carrying hypomorphic alleles of DNMT1 [GeneID=1786]. Full description or abstract Previous studies have shown that tumor progression in the transgenic adenocarcinoma of mouse prostate (TRAMP) model is characterized by global DNA hypomethylation initiated during early-stage…

We are seeking multiple Experimental and Bioinformatics research positions (including Postdoctoral Research Fellows and Research Associate) to join the Alzheimer’s Network Medicine and Artificial Intelligence (AI) research group (www.lerner.ccf.org/gmi/cheng/) led by Dr. Feixiong Cheng at the Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, and Department of Molecular Medicine at…

Researchers at the University of Illinois at Chicago and Washington University describe an online database called OncoDB, designed for analyzing large cancer datasets to detect gene expression shifts and viral infections with potential ties to cancer, such as human papillomavirus. The current version of the resource contains data for more…

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…

error while running predictdb tutorial 0 Hello, I am trying to use predictdb tutorial. The link is: github.com/hakyimlab/PredictDB-Tutorial When I run gtex_tiss_chrom.R script, it throws an error Error in file(file, “rt”) : cannot open the connection Calls: main …get_filtered_snp_annot -> %>% -> distinct -> filter -> read.table -> file In…

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…

(Senior) Bioinformatician            AL Solutions are searching for a Bioinformatician or Senior Bioinformatician to work within the Data Science team of an innovative start-up Biotechnology company in Cambridge. This company are developing innovative medicines within the Oncology & Immunology space. Your position will be to drive the development of computational tools…

What exactly is RNA-seq probe? 0 Hi all, I’m a long time lurker, but this is my first post here, so I’m sorry if I do something wrong or post something that is against the rule, I’m new to RNA-seq analysis. But I’ve downloaded a huge dataset with matched RNA-seq…

GTEX – how to upload more than one rsIDs to get gene expression or eQTL information 1 Hi everyone, I am trying to see how my variants affect the host gene -or other eQTLs- to see the direction of effect basically. I looked on GTEx but I only found the…

GTEX eQTLs’ extraction 0 Hello everyone, I am a still a student and I am new to this forum, but I would need help regarding GTEX and how to work with it. I was given a task, which includes finding and extracting eQTLs for specific genes from the GTEX portal…

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

Introduction BC is the most common cancer among women that is responsible for the most of the cancer-related death in worldwide.1 The occurrence of BC accounts for 7–8% of the entire number of malignant tumors.2 Accumulating evidence have shown that immunoreaction plays an important role in oncogenesis and progression.3,4 However,…

Introduction Primary liver cancer, including hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma, is the sixth most commonly diagnosed cancer and the fourth leading cause of cancer-related deaths worldwide.1 High metastasis and recurrence rates, as well as limited treatment options, lead to the poor prognosis of advanced HCC.2 Among patients diagnosed with…

Counting the number of SNPs (VCF) for each genomic coordinates (BED) 1 I want to count the number of recorded variations for each genomic coordinates of a .bed file from the corresponding .vcf file. I guess it should be solved by vcftools, but I could not find any suitable option…

We are currently looking for a Bioinformatics Scientist to join a leading biotech company based in the Cambridge area. As the Bioinformatics Scientist you will drive the development of computational tools and perform omics data analysis to support target identification and therapeutics development platforms KEY DUTIES AND RESPONSIBILITIES: Your duties…

IGM Biosciences (Nasdaq: IGMS) is a clinical-stage biotechnology company focused on creating and developing engineered IgM antibodies. IgM antibodies have inherent properties that we believe may enable them to improve upon the efficacy and safety of IgG antibodies in multiple therapeutic applications. We have created a proprietary IgM antibody technology…

Bioinformatics Biomedical Scientist – Bilsborough Lab – Inflammatory Bowel Diseases Drug Discovery and Development Apply Now Share Requisition # HRC0697538 Join us in accelerating the pace of research and discovery within our unique IBD3 lab! Cedars-Sinai provides virtually every known gastroenterologic analytical procedure and treatment…

Forum:Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols 2 Published in the RNA Journal in 2020 – this paper argues that if the original RNA amount in the different samples is different, TPM should not be used to find differentially expressed genes. www.ncbi.nlm.nih.gov/pmc/articles/PMC7373998/ Seems like…

About Aro BioTx Join the team at Aro Biotherapeutics creating breakthrough biotherapeutics based on Centyrin oligonucleotide conjugates. Centyrins are small protein domains based on the fibronectin domains of human Tenascin C that combine the affinity and specificity properties of antibodies with the stability and tissue penetration properties of small molecules….

We are currently looking for a Bioinformatics Scientist to join a leading biotech company based in the Cambridge area. As the Bioinformatics Scientist you will drive the development of computational tools and perform omics data analysis to support target identification and therapeutics development platforms KEY DUTIES AND RESPONSIBILITIES: Your duties…

TCGA data: low / high grade ovarian cancer 0 Dear All, I have downloaded ovarian cancer annotation data from the TCGA using the TCGAbiolinks package (recount2 data) as follows: ovary_rec2_gtex <- TCGAquery_recount2(project=”gtex”, tissue = “ovary”) tcga_sampleAnnot <- data.frame(ovary_rec2_tcga_scaled@colData) I can check the cancer type with command like this one unique(tcga_sampleAnnotgdc_cases.project.name)…

TMM followed by inverse normal transform 0 Hey all, I am following a protocol from a paper that uses the following pre-processing procedure: a. Read counts were normalized between samples using TMM (Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome…

How to download GTEx figure from USCS genome browser 1 Hello, Unfortunately the GTEx images are generated on demand then erased later. In case it helps, these are dynamically generated by R from the track data. We can help with finding the exact parameters if you are interested. The temporary…

Differential expression analysis between normal/cancer on recount2 data 0 Hi everyone, I have download GTEX data and TCGA data (only tumor samples available) for a given cancer type using the “recount” R package. After having filtered the genes that are in common between the 2 datasets, I would like to…

Download TCGA and GTEX data from Xena toilHub for (full genome but for 1 cancer/tissue type) 0 Dear All, I would like to download TCGA and GTEX gene expression data for ovarian cancer and ovary respectively from the Xena toilHub platform (all genes; RSEM expected counts). However, I only found…

Rancho Biosciences is seeking a RShiny bioinformatics expert to provide support for a range of projects which include the development of R-Shiny applications, managing NGS data associated with clinical and metadata organization. Work from home while supporting high impact pharmaceutical, academic and institutional science programs. We are specifically looking for…

normalization two different datasets tcga vs gtex 0 using tcga and gtex to look for lncrna DE (using raw files) – what are the best ways to normalize? deseq2 and edger? also if i want to look at lncrnas of specific chromosomes, how should i approach normalization? tcga gtex normalization…