Category: gtex

(Senior) Bioinformatician job with AL2S3 LTD

(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…

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What exactly is RNA-seq probe?

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…

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how to upload more than one rsIDs to get gene expression or eQTL information

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…

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GTEX eQTLs’ extraction

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…

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Bioconductor – Bioconductor 3.14 Released

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,…

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LncRNA MIAT services as a noninvasive biomarker

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,…

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H/ACA snoRNP gene family as diagnostic/prognostic biomarkers

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…

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Counting the number of SNPs (VCF) for each genomic coordinates (BED)

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…

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Job Details

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Bioinformatics Scientist job with Hyper Recruitment Solutions (HRS)

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…

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Bioinformatics Research Associate II/III, Immuno-Oncology Job Opening in Mountain View, CA at IGM Biosciences

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…

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Bioinformatics Biomedical Scientist – Bilsborough Lab

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…

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Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols

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…

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Aro Biotherapeutics hiring Investigator, Genetics & Bioinformatics in Philadelphia, Pennsylvania, United States

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….

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Bioinformatics Scientist – reed.co.uk

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…

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low / high grade ovarian cancer

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)…

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TMM followed by inverse normal transform

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…

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How to download GTEx figure from USCS genome browser

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…

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Differential expression analysis between normal/cancer on recount2 data

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…

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Download TCGA and GTEX data from Xena toilHub for (full genome but for 1 cancer/tissue type)

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…

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Bioconductor – cageminer (development version)

DOI: 10.18129/B9.bioc.cageminer     This is the development version of cageminer; to use it, please install the devel version of Bioconductor. Candidate Gene Miner Bioconductor version: Development (3.14) This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users…

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Rancho BioSciences hiring RShiny Scientist/Bioinformatics in San Diego, California, United States

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…

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normalization two different datasets tcga vs gtex

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…

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