Tag: tcga

Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…

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Impact of sweet, umami, and bitter taste receptor (TAS1R and TAS2R) genomic and expression alterations in solid tumors on survival

Despite being best known for their role in taste sensing1, T2Rs and T1Rs have been identified in various extra-oral tissues where they serve diverse chemosensory roles17,18,19,20,21,22,48. Emerging data on the role of taste receptors in malignancy led us to explore the genetic and expression alterations for solid tumors and implications…

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Bioconductor – ComplexHeatmap

DOI: 10.18129/B9.bioc.ComplexHeatmap     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ComplexHeatmap. Make Complex Heatmaps Bioconductor version: 3.14 Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly…

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Role of CD68 in tumor immunity and prognosis prediction in pan-cancer

Expression of CD68 in pan-cancer First, to fully clarify the expression of CD68 in pan-cancer, we matched the GTEx normal samples with TCGA tumor samples (Fig. 1A). We found that the levels of CD68 were significantly elevated (P < 0.01) in colon adenocarcinoma (COAD), glioblastoma multiforme (GBM), kidney renal clear cell carcinoma (KIRC),…

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Problem in getting SNAI1 gene in prostate DEG table

Problem in getting SNAI1 gene in prostate DEG table 0 Hello everyone, would you please help me I have got prostate DEGs by TCGAbiolinks package but I couldn’t get SNAI1 gene in my DEG table. I wonder why it does happen. First I normalized it and then I filtered it,…

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Molecular analysis of TCGA breast cancer histologic types

Breast cancer is classified into multiple distinct histologic types, and many of the rarer types have limited characterization. Here, we extend The Cancer Genome Atlas Breast Cancer (TCGA-BRCA) dataset with additional histologic type annotations, in a total of 1063 breast cancers. We analyze this extended dataset to define transcriptomic and…

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N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance | Military Medical Research

Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…

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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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HTSeq Counts no longer available

HTSeq Counts no longer available 1 @vm-21340 Last seen 8 hours ago Brazil I’m working with breast cancer expression data from the TCGA-BRCA project. All my scripts were written to retrieve HTSeq counts from GDC, but they seem to have been removed from the GDC Data Portal. When using GDCquery,…

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GDCquery_Maf error

GDCquery_Maf error 0 @76e1237b Last seen 1 day ago Singapore Hi all, I really need some help. I am trying to run GDCquery_Maf which worked fine until yesterday. Now I get the following error: Error in GDCquery(paste0(“TCGA-“, tumor), data.category = “Simple Nucleotide Variation”, : Please set a valid workflow.type argument…

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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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Xena TCGA TARGET TCGx RNAseq Data

Zenodo DOI Badge DOI 10.5281/zenodo.6323594 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg)](https://doi.org/10.5281/zenodo.6323594) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg :target: doi.org/10.5281/zenodo.6323594 HTML <a href=”https://doi.org/10.5281/zenodo.6323594″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg Target URL doi.org/10.5281/zenodo.6323594 Read more here: Source link

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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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Genomic and epigenomic alterations of the basal-like prognostic biomarkers.

a) Heatmap with dendrogram representing the unsupervised hierarchical clustering analysis based on CNVs data of TCGA-BRCA patients. The rows in the heatmap represent the 11 basal-like prognostic biomarkers. The columns correspond to basal-like and luminal A TCGA-BRCA patients: basal-like are indicated in dark blue and luminal A in green. The…

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RNA-Seq HTseq galaxy DE analysis

RNA-Seq HTseq galaxy DE analysis 0 Hi friends I have htseq data from TCGA. it contains patients name in first row and genes in first column : 200 columns and 20000 rows. I dont want deseq2 in R. this needs to be done in galaxy. my question is how to…

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How can you score CNV for each sample (with TCGA data)?

How can you score CNV for each sample (with TCGA data)? 0 Hi, I’m looking at TCGA CNV data, and trying to get a sense of how copy number altered each sample is. TCGA gives “Segment_Mean” values for varying sized regions of the genome for each sample, which to my…

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Identification of key mutations in central nervous diffuse large B-cell lymphoma (DLBCL) by comprehensive analysis between sequencing and TCGA database

Background: Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin’s lymphoma, and hence, a comprehensive understanding based on the gene expression profile is imperative. Although several studies have identified some critical mutant genes of DLBCL, the disease in the central nervous system has not been investigated clearly….

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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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Accepted r-bioc-tcgabiolinks 2.22.4+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sun, 30 Jan 2022 18:02:27 +0100 Source: r-bioc-tcgabiolinks Architecture: source Version: 2.22.4+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-tcgabiolinks (2.22.4+dfsg-1) unstable; urgency=medium . * New upstream version * dh-update-R to update Build-Depends…

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Identification of Novel Diagnostic Biomarkers in Prostate Adenocarcinoma Based on the Stromal-Immune Score and Analysis of the WGCNA and ceRNA Network

This article was originally published here Dis Markers. 2022 Jan 15;2022:1909196. doi: 10.1155/2022/1909196. eCollection 2022. ABSTRACT Prostate cancer is still a significant global health burden in the coming decade. Novel biomarkers for detection and prognosis are needed to improve the survival of distant and advanced stage prostate cancer patients. The…

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Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….

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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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The Identification of Prognostic and Metastatic Alternative Splicing in Skin Cutaneous Melanoma

Skin cutaneous melanoma (SKCM) is a type of highly invasive cancer originated from melanocytes. It is reported that aberrant alternative splicing (AS) plays an important role in the neoplasia and metastasis of many types of cancer. Therefore, we investigated whether ASEs of pre-RNA have such an influence on the prognosis…

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Associate Director, Bioinformatics Job Opening in Wilmington, DE at Incyte Corporation

Incyte is a biopharmaceutical company focused on the discovery, development, and commercialization of novel medicines to meet serious unmet medical needs in oncology and inflammation and autoimmunity. Incyte is committed to the rigorous pursuit of research and development excellence to improve the lives of patients, make a difference in health…

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Establishment of sunitinib-resistant CDX model of ccRCC

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

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Hypoxic Characteristic Genes Predict Response to Immunotherapy for Urothelial Carcinoma

This article was originally published here Front Cell Dev Biol. 2021 Nov 25;9:762478. doi: 10.3389/fcell.2021.762478. eCollection 2021. ABSTRACT Objective: Resistance to immune checkpoint inhibitors (ICIs) has been a massive obstacle to ICI treatment in metastatic urothelial carcinoma (MUC). Recently, increasing evidence indicates the clinical importance of the association between hypoxia…

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Experimental and Meta-Analytic Validation of RNA Sequencing Signatures for Predicting Status of Microsatellite Instability

doi: 10.3389/fmolb.2021.737821. eCollection 2021. Affiliations Expand Affiliations 1 Laboratory For Clinical and Genomic Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia. 2 Moscow Institute of Physics and Technology, Dolgoprudny, Russia. 3 OmicsWay Corp., Walnut, CA, United States. 4 Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia. 5…

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Index of /runs/gdc/report_2018_02_16

Name Last modified Size Description Parent Directory   –   TCGA-ACC.2018_02_16.diced_metadata.tsv 2018-02-16 01:06 250K   TCGA-ACC.2018_02_16.high_res.heatmap.png 2018-02-16 01:08 73K   TCGA-ACC.2018_02_16.low_res.heatmap.png 2018-02-16 01:08 37K   TCGA-ACC.2018_02_16.sample_counts.tsv 2018-02-16 01:06 142   TCGA-BLCA.2018_02_16.diced_metadata.tsv 2018-02-16 01:06 1.2M   TCGA-BLCA.2018_02_16.high_res.heatmap.png 2018-02-16 01:08 90K   TCGA-BLCA.2018_02_16.low_res.heatmap.png 2018-02-16 01:08 53K   TCGA-BLCA.2018_02_16.sample_counts.tsv 2018-02-16 01:06 201  …

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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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r – ggplot: Try to plot boxplots with geom_rect on its background, but keep having error with object “variable” not found

I was almost desperate with this error after working on this for 4 hrs, googled and looked from past posts already. Here is my data structure: str(tcga_exp) ‘data.frame’: 11775 obs. of 5 variables: $ cohort: chr “BRCA-Basal.Tumor” “BRCA-LumA.Tumor” “BRCA-LumB.Tumor” “BRCA-LumA.Tumor” … $ exp : num 6.35 5.54 6.56 5.05 5.98…

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Identification of lipid metabolism-associated gene signature

Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…

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About outliers and non -separated samples in PCA

About outliers and non -separated samples in PCA 0 Hi all, I have plotted PCA for my samples(Tumor and Normal) in some cancer types. I have used the HTSeq-counts data from TCGA. Then I’ve normalized them by DESeq2 and the total normalized counts are in cnt dataframe. Head of cnt:…

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raw counts in TCGA RNA-seq data

raw counts in TCGA RNA-seq data 3 HI, I want to find differential expressed genes in TCGA datasets by edgeR. I used RNA-seq data measured by raw_counts as input. In the file with suffix “.rsem.isoforms.results”, there are three columns which are isoform_id, raw_count and scaled_estimate. Below is the first 15…

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TCGA transcriptome data to R (DESeq2)

This seems to be frequently asked question, so here is a robust method to fully recapitulate the counts given by TCGA and port it to DESeq2. Why the long way? Tanya and I noticed via TCGA-Biolinks and Firehose did not generate the full count matrix. ~5-10% of genes were missing…

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need some help on how to use DESeq2 for TCGA data

need some help on how to use DESeq2 for TCGA data 0 Hello, I am sorry for this newbie question, but I spent all morning trying to find it out but can’t find a clear answer anywhere. I want to normalise RNA seq data from TCGA using DESeq2. I use…

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Convert Log2 (FPKM+0.001) to FPKM in an expression matrix obtained from TCGA

Convert Log2 (FPKM+0.001) to FPKM in an expression matrix obtained from TCGA 0 Hi, I have downloaded TCGA data generated from TOIL RNA-seq pipeline. Basically, it is log2(x+0.001) transformed transcript-level expression values (FPKM) matrix. Link to dataset I intend to analyze isoform switching using IsoformSwitchAnalyzeR which won’t work with log2…

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BioSpace hiring Associate Bioinformatics Scientist in Cambridge, Massachusetts, United States

About Us…Obsidian Therapeutics is pioneering engineered cell and gene therapies to deliver transformative outcomes for patients. Obsidian’s programs apply our CytoDriveTM technology in Cell and Gene therapy products to control expression of proteins for enhanced therapeutic efficacy and safety. Obsidian’s lead program is currently in preclinical development for the treatment…

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Help with TCPA Protein Names

Help with TCPA Protein Names 0 Hello everyone, I would want to correlate protein expression and mRNA expression in my breast cancer research. I downloaded L4 level RPPA data from the TCPA portal: tcpaportal.org/tcpa/download.html, and got a protein expression matrix which is great. However, I was baffled by the protein…

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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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How to create a mutation landscape (waterfall) plot with GenVisR

This tutorial makes use of the GenVisR package. Please cite: Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL, Griffith M. 2016. GenVisR: Genomic Visualizations in R. Bioinformatics. pii: btw325. [Epub ahead of print]PubMed | Bioinformatics Journal | BioRxiv | Bioconductor | GitHub Note: A more comprehensive…

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How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons

How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons 1 Dear community, I am totally new to TCGA and Bioconductor and I am really confused how to obtain more clinical data (e.g. for survival analysis, gender, RNA-seq read count data, …) from some cases I got. For every “patient”…

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Bioinformatics Analyst II – Bethesda

PROGRAM DESCRIPTION The Advanced Biomedical Computing Center (ABCC) is a part of the Biomedical Informatics and Data Science (BIDS) Program at Leidos Biomedical Research, Inc. The ABCC provides technology development, scientific consultation, collaboration and training, and high-performance computing support to the NCI and NIH scientists and staff. KEY ROLES/RESPONSIBILITIES The…

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How Has Technology Influenced The Life Sciences Industry

We all know how computers and microchips have brought a technological revolution. Different software has been used to improve businesses, and even smartphones are helping with work and education. The life sciences industry is a booming area, and it continues to grow and expand with every passing decade. Once again…

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question about TCGA survival data

question about TCGA survival data 3 Many TCGA samples have three rows in their clinical data that may be of interest for survival analysis: days to death, days to last follow-up, and days to sample procurement. My questions are, in this data, what does day 0 refer to, and what…

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Nucleic Acids Research Papers on OncoDB, mBodyMap, Genomicus

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…

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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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TCGAbiolinks methylation data normalization

TCGAbiolinks methylation data normalization 0 hello! I downloaded TCGA methylation data using TCGAbiolinks package in R. <h6>#############code</h6> query<-GDCquery(project = “TCGA-READ”, data.category = “DNA Methylation”, legacy = F, platform = “Illumina Human Methylation 450”, sample.type=c(“Primary Tumor”)) GDCdownload(query) data<-GDCprepare(query) data<-SummarizedExperiment::assay(data) <h6>#</h6> I want to use this data to train and test my…

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When I change samples grouping for normalization by DESeq2 I get different results, Why?

When I change samples grouping for normalization by DESeq2 I get different results, Why? 0 Hi all I have downloaded the raw counts of RNA-Seq from TCGA for DE analysis. the number of primary tumor samples was 223 and the normal adjacent tissue was 41. I have performed the normalization…

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When do we consider TCGA mRNA and miRNA data as matched samples?

When do we consider TCGA mRNA and miRNA data as matched samples? 0 Hi all, I am wondering about the standard practice for matching TCGA mRNA and miRNA data based on their TCGA barcodes. In specific, which portion of the IDs should match? would it suffice for participant’s IDs to…

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Natera hiring Senior Bioinformatics Scientist in San Carlos, California, United States

Successful applicants for this position must be fully vaccinated against COVID-19 as a condition of employment. Vaccine verification will be required. Position Summary Natera is currently seeking a Senior Bioinformatics Scientist to join our Bioinformatics Research & Development team with a focus on cancer early detection. Natera’s mission is to…

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Do I have to separate my interest genes from my count matrix and then perform differential expression analysis for them?

Do I have to separate my interest genes from my count matrix and then perform differential expression analysis for them? 0 Hi all, I am trying to study the differential expression of my interest genes in colon cancer. First, I’ve downloaded the RNA-Seq raw counts from TCGA and have built…

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Bioinformatics scientist (Full-time/Permanent) for the analysis of multiomics data in oncology

Position of Bioinformatics scientist (Full-time/Permanent) for the analysis of multiomics data in oncology, at Evotec Toulouse (France) to be filled as soon as possible. www.evotec.com/en General Summary : For our site in Toulouse, France, we have an exciting opportunity for a dedicated and professional Bioinformatics Scientist – Full time and…

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Comprehensive analysis of the prognosis and biological significance for IFIT family in skin cutaneous melanoma by Yuxiong Jiang

Interferon-induced protein with tetratricopeptide repeats (IFITs) genes, consisting of four members named IFIT1, IFIT2, IFIT3 and IFIT5, are involved in the progression of multiple cancer types, but their roles in skin cutaneous melanoma (SKCM) are still largely unknown. The TCGA-SKCM dataset, GSE15605 dataset and GSE100508 dataset were obtained in our…

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r – GDCprepare() returns Error in function (classes, fdef, mtable)

I have downloaded Proteome Profiling data from the TCGA-LGG project with the Bioconductor package TCGAbiolinks. Then I have the following error when running GDCprepare: library(“TCGAbiolinks”) query_lgg = GDCquery( project = “TCGA-LGG”, data.category = “Proteome Profiling”, sample.type = “Primary Tumor”, legacy = FALSE) #> ————————————– #> o GDCquery: Searching in GDC…

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When I convert the Ensembl IDs to gene symbols, why lots of genes are duplicated?

Hi all, I have raw counts of samples in a dataframe. The row names is Ensembl ID and I want to convert them to a gene symbol. So I’ve run the code below. query <- GDCquery(project = “TCGA-COAD” , data.category = “Transcriptome Profiling” , data.type = “Gene Expression Quantification”, workflow.type…

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Using TCGA RSEM data to calculate isoform expression

Using TCGA RSEM data to calculate isoform expression 0 Hello everyone, I have download the TCGA RNAseq RSEM data about isoform expression. I would like to check which one of the isoforms of my gene is the one expressed the most. Can I directly use the RSEM values to conclude…

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(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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Different Result in Univariate Cox Regression and Multivariate Cox Regression

Different Result in Univariate Cox Regression and Multivariate Cox Regression 0 Hi, everyone! I used limma package in R to find different expression genes in a TCGA dataset, and then I used the univariate cox regression to find different expressed genes releated to the overall survival, using the P value<0.05,…

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Bioconductor – RTCGA.mRNA

DOI: 10.18129/B9.bioc.RTCGA.mRNA     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see RTCGA.mRNA. mRNA datasets from The Cancer Genome Atlas Project Bioconductor version: 3.11 Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from gdac.broadinstitute.org/. Data format…

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Why can I not reproduce some of TCGA’s MAF file contexts from the coding sequences of the mutated genes?

Why can I not reproduce some of TCGA’s MAF file contexts from the coding sequences of the mutated genes? 0 I am working with the mc3.v0.2.8.PUBLIC.maf.gz MAF file (downloaded from here) and I need to analyze the coding sequences (CDS) of the mutated genes. I only do this for SNP…

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Discovery and construction of prognostic model for clear cell renal cell carcinoma based on single-cell and bulk transcriptome analysis

This article was originally published here Transl Androl Urol. 2021 Sep;10(9):3540-3554. doi: 10.21037/tau-21-581. ABSTRACT BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is the most common malignant kidney tumor in adults. Single-cell transcriptome sequencing can provide accurate gene expression data of individual cells. Integrated single-cell and bulk transcriptome data from ccRCC…

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Exploration of Prognostic Biomarkers of Muscle-Invasive Bladder Cancer (MIBC) by Bioinformatics

This article was originally published here Evol Bioinform Online. 2021 Oct 28;17:11769343211049270. doi: 10.1177/11769343211049270. eCollection 2021. ABSTRACT We aimed to discover prognostic factors of muscle-invasive bladder cancer (MIBC) and investigate their relationship with immune therapies. Online data of MIBC were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression…

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Bioinformatics analysis to screen DNA methylation-driven genes for prognosis of patients with bladder cancer

This article was originally published here Transl Androl Urol. 2021 Sep;10(9):3604-3619. doi: 10.21037/tau-21-326. ABSTRACT BACKGROUND: Bladder cancer (BLCA) is the most prevalent tumor affecting the urinary system, and has contributed to a rise in morbidity and mortality rates. Herein, we sought to identify the methylation-driven genes (MDGs)of BLCA in an…

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Research Engineer (RE123)

Job:Research Engineer (RE123) 0 Context And Mission Professor Nataša Pržulj is looking for a Research Support Engineer to work in her Integrative Computational Network Biology (ICONBI) group (overview of the group is at www.bsc.es/discover-bsc/organisation/scientific-structure/integrative-computational-network-biology-iconbi).The post-holder will participate in the process of finding, designing and implementing new algorithms, Data Science and…

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How to define low, medium or high expression of a microRNA?

How to define low, medium or high expression of a microRNA? 0 Hello everyone, I am working with TCGA tumor samples, however the base from where i retrieved information regarding microRNA expression in those samples is the OncoMir Cancer Database (absolute data view) Now i have the expression of the…

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Converting Ensembl gene id to Gene symbol

Converting Ensembl gene id to Gene symbol 0 Hi all, As mentioned earlier in this post, I tried to convert the Ensembl gene ids to the Gene symbol. I didn’t receive any error by the code below but the nrow of ens_to_symbol_biomart is 55605 and the length of ens is…

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Box plot for rna seq data

Box plot for rna seq data 1 Hi friends I plotted this box-wisker for TCGA HTSeq data in R. I want to have harf of them as red and half as blue (control vs treatment groups). or is there any better way for boxplot? How can I do that? I…

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TCGA patient death dates

TCGA patient death dates 0 Hi everyone, I’ve been looking at the TCGA clinical data, queried using TCGAbiolinks: allproj <- getGDCprojects() projs <- allproj[startsWith(allproj$id, ‘TCGA’),]$id clin <- lapply(projs, FUN = GDCquery_clinic, ‘clinical’) I was surprised to see some patients with death dates before TCGA data collection started in ~2006. There…

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3 ways how DNA sequencing could be beneficial for cancer treatment

Cancer is caused by changes in DNA – the genetic material that controls cell function. In most cases, cancer is the result of uncontrolled cell division due to abnormalities in the DNA. Some of these changes may be inherited, but some may be sporadic. Each type of cancer may have…

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Discrepancy between samtools bedcov and pysam.count

I’m writing a new version of a tool and I’m trying to implement some functionality using pysam that was previously implemented using samtools bedcov. For example, here is a sample output of samtools bedcov test.bed tcga_test.bam -Q 50: chr19 50858094 50858095 64004 chr19 50858128 50858129 63170 chr19 50858162 50858163 51889…

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Bioinformatics Data Science Analyst Job in Toronto for University Health Network

Job Posting #886746 Position: Bioinformatics Analyst Site: Toronto General Hospital Research InstitueDepartment: Multi Organ TransplantReports to: Principal InvestigatorHours: 37.5 per weekSalary Scale: $62,166 – $77,688 per annum (commensurate with experience and consistent with UHN Compensation Policy)Status: Temporary Full-time University Health Network (UHN) is looking for an experienced professional to fill…

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TCGA-BRCA surgery date in clinical data

Hi, I’m trying to make a treatment chronology for patients in the TCGA-BRCA database and this rapidly became a big mess… I’m using TCGAbiolinks on R. I’ve managed to find the start/stop days after diagnosis for drugs and radiation therapy beginning/ending through clinical info (“clinical_drug_brca”, “clinical_radiation_brca”). I’ve also managed to…

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PER1 as a Tumor Suppressor Attenuates Breast Cancer

Introduction Breast cancer is one of the most common malignancies in women, with a high mortality rate around the world.1,2 Although multidisciplinary therapeutic strategies, including surgical resection, chemoradiotherapy, endocrine and anti-HER2 therapy, have made substantial progress over the past decade, there are still a considerable proportion of breast cancer patients…

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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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Is it possible to programmatically download the tables containing mutations, structural variants and CNAs shown in the summary section of an specific patient?

cBioPortal: Is it possible to programmatically download the tables containing mutations, structural variants and CNAs shown in the summary section of an specific patient? 0 Hello everyone! I’m currently working with the TCGA-BRCA dataset, using the data provided by both GDC Portal and cBioPortal. There is some processed data displayed…

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TCGA survival by gene expression. Gene is missing everywhere I look, but should be possible?

TCGA survival by gene expression. Gene is missing everywhere I look, but should be possible? 0 Hello, I am trying to generate TCGA survival plots with gene expression data. I found a few interesting guides out there, but the genes I am interested in don’t work. The genes I want…

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Identification of Hub Genes Associated With Clear Cell Renal Cell Carcinoma by Integrated Bioinformatics Analysis

This article was originally published here Front Oncol. 2021 Sep 30;11:726655. doi: 10.3389/fonc.2021.726655. eCollection 2021. ABSTRACT BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is a common genitourinary cancer type with a high mortality rate. Due to a diverse range of biochemical alterations and a high level of tumor heterogeneity, it…

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Clinical Impact of X-Ray Repair Cross-Complementary 1 (XRCC1) and the

Plain Language Summary Colorectal cancer progresses through a well‑defined series of transformations from normal colonic epithelial cells to precursor adenoma lesions that eventually evolve into increasingly more invasive and malignant stages. An improved understanding of the genetic and molecular drivers of colorectal cancer, especially the progression of adenoma to carcinoma,…

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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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A TME-Related Signature as a Biomarker in Liver Cancer

Introduction As one of the most frequent causes of cancer deaths across the globe, liver cancer, characterized by high mortality, recurrence, metastasis and poor prognosis, is the only one of the top five deadliest cancers to have an annual percentage increase in occurrence.1 Surgery, local destructive therapies, and liver transplantation…

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For DE analysis, should I exclude all the samples that don’t have the data of normal tissue?

For DE analysis, should I exclude all the samples that don’t have the data of normal tissue? 0 Hi I have downloaded the RNA-Seq data of my interest cancer type from TCGA. most of the samples are the primary tumor and just a few of them are the normal tissue….

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Is it representative to use the minimal matched data of RNA-Seq in TCGA?

Is it representative to use the minimal matched data of RNA-Seq in TCGA? 0 Hi all, As far as I understood, the number of “solid tissue normal” data in TCGA is minimal, and given this, I have two questions: For DE analysis that we need the matched data of normal…

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Download all cases from TCGAbiolinks

Hi all, I would like to download the bulk RNA-seq data for all patients in the TCGA-LUAD cohort using TCGAbiolinks. Does this exist as a single matrix? I have read the package vignette and can download individual cases however does TCGAbiolinks facilitate downloading a single matrix of all the patients?…

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Identification of antineoplastic agents for oral squamous cell carcinoma: an integrated bioinformatics approach using differential gene expression and network biology

Abstract Oral squamous cell carcinoma (OSCC) is the most common malignant epithelial neoplasm and anatomical subtype of head and neck squamous cell carcinoma (HNSCC) with an average 5-year survival rate of less than 50%. To improve the survival rate of OSCC, the discovery of novel anti-cancer drugs is urgently needed….

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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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Bioconductor – RTCGA.rnaseq

DOI: 10.18129/B9.bioc.RTCGA.rnaseq     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see RTCGA.rnaseq. Rna-seq datasets from The Cancer Genome Atlas Project Bioconductor version: 3.10 Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from gdac.broadinstitute.org/. Rna-seq data format…

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convert TCGA hg38 maf to hg 19 maf

convert TCGA hg38 maf to hg 19 maf 1 I tried to use maf2vcf to convert and used the vcf2vcf with remap function, but while doing that in the final file all data is missing (except for #CHROM POS ID REF ALT QUAL FILTER GT:AD:DP ) How do I convert…

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Type of Normalization done to TCGA level 3 Methylation Data

Type of Normalization done to TCGA level 3 Methylation Data 0 Hello! I have TCGA level 3 methylation data on CHOL and I want to replicate DMR analysis procedure in a paper I am reading but using different data than was used. Now, I know from TCGAs website that level…

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Bioinformatician job with Volt | 1239582

I’ve partnered with a global biopharmaceutical company, who have developed a platform to provide clinical drug screens to optimise treatment decisions in patients within cancer, alongside a biobank of (PDC) models that enables them to offer screening to support pharmaceutical drug development. They’re looking for a Bioinformatician to develop, maintain…

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lncRNA quantification featurecounts

lncRNA quantification featurecounts 0 Hi everyone, I want to analyze the differential expression of lncRNA using TCGA data processed with RSubread (FPKM and TPM, gene-level data, see here: www.ncbi.nlm.nih.gov/pmc/articles/PMC4804769/). Is there any way to filter only lncRNA gene IDs from the output of featurecounts? And would it be relevant to…

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Is it advisable to input a count matrix that consists of reads aligned using different algorithms (HT-Seq and Salmon)?

Hello! First of all, thank you for the great package and the excellent documentation that supports it, much appreciated! Sadly, I could not find an answer to my problem, so I wanted to ask here. I have two different bulk RNA-seq datasets, one obtained from TCGA using the TCGAbiolinks package,…

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Identification of immunization-related new prognostic biomarkers for papillary renal cell carcinoma by integrated bioinformatics analysis

This article was originally published here BMC Med Genomics. 2021 Oct 7;14(1):241. doi: 10.1186/s12920-021-01092-w. ABSTRACT BACKGROUND: Despite papillary renal cell carcinoma (pRCC) being the second most common type of kidney cancer, the underlying molecular mechanism remains unclear. Targeted therapies in the past have not been successful because of the lack…

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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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Bioconductor Case Studies Use R

Bioconductor Case Studies Use R Analysing time course microarray data using Bioconductor MeV+R: using MeV as a graphical user interface for Omic association studies with R and Bioconductor (eBook Results: We describe RTNsurvival, an R/Bioconductor package that calculates regulon activity profiles…

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TCGA Isoform Expression Data

TCGA Isoform Expression Data 1 Hello everyone, Is there anyone who could shortly enlighten me on how TCGA generates their isoform expression data briefly ? You should feel free to leave any informative links as well in the comments section. Thank you i n advance! reads Rnaseq isoform tcga quantification…

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Twist Bioscience Expands Exper – GuruFocus.com

Twist Bioscience Corporation (NASDAQ: TWST), a company enabling customers to succeed through its offering of high-quality synthetic DNA using its silicon platform, today announced an expansion of its expert-led Alliance Panel product offering. Designed through collaboration with world-leading experts, Twist Alliance Panels combine validated content with Twist next-generation sequencing (NGS)…

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Twist Bioscience Expands Expert Custom Alliance Panel Offering

– Ready to Order Clinically Validated, Expert-Designed Panels Offer Important Tools for Multiple Research Applications – – Twist Alliance Pan-Cancer Methylation Panel Launched – SOUTH SAN FRANCISCO, Calif.–(BUSINESS WIRE)– Twist Bioscience Corporation (NASDAQ: TWST), a company enabling customers to succeed through its offering of high-quality synthetic DNA using its silicon…

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Cytochrome P450-2D6: A novel biomarker in liver cancer health disparity

This article was originally published here PLoS One. 2021 Oct 1;16(10):e0257072. doi: 10.1371/journal.pone.0257072. eCollection 2021. ABSTRACT Liver cancer morbidity and mortality rates differ among ethnic groups. In the United States, the burden of liver cancer in Asian Americans (AS) is higher compared to Caucasian Americans (CA). Research on liver cancer…

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How to pick the threshold of segment mean values in copy number variation data?

How to pick the threshold of segment mean values in copy number variation data? 1 Hello, everyone! The segment_mean in copy number variation data of TCGA describe the log-transform copy number value of specific chromosome segment. I want to know how to pick the threshold to select abnormal fragments? Thanks,…

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