Tag: deseq2

Barrier-to-autointegration factor 1 promotes gammaherpesvirus reactivation from latency

Biosafety statement All experiments with cell lines and viral infections were carried out in a Biosafety Level 2 facility under the approval of the Biosafety Office in the Department of Environment, Health and Safety and the Institutional Biosafety Committee at the University of North Carolina at Chapel Hill. The laboratory…

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Bioconductor – DiffBind

DOI: 10.18129/B9.bioc.DiffBind     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DiffBind. Differential Binding Analysis of ChIP-Seq Peak Data Bioconductor version: 3.15 Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions….

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Different summary() and results() values in DeSeq2

Different summary() and results() values in DeSeq2 2 @e7ba24a7 Last seen 2 hours ago Germany I have run DeSeq2 in 2 different devices using the same count data and metadata tables, however when running the summary and results I get different values. I made sure the files are read correctly,…

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Scholarships and Career Opportunities: Postdoctoral researcher in bioinformatics

 Lund University was founded in 1666 and is repeatedly ranked among the world’s top 100 universities. The University has around 46 000 students and more than 8 000 staff based in Lund, Helsingborg and Malmö. We are united in our efforts to understand, explain and improve our world and the…

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DESeq2 results function runs very slow on Windows 10

Hi, I have bulk RNA-seq data that I analyze with DESeq2. The code I have is the following. dds <- readRDS(“DESeqDataSet.rds”) design(dds) = ~groupSSc dds <- estimateSizeFactors(dds) dds <- DESeq(dds) BC_SSc <- results(dds, contrast=c(“groupSSc”, “SSc”, “HC”), independentFiltering=TRUE, alpha=0.05, pAdjustMethod=”BH”, parallel=TRUE) The problem arises with the results function. When I run…

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Which genes are outliers in DESeq2?

Which genes are outliers in DESeq2? 2 @c2575e9b Last seen 21 hours ago United States Hello! I had a question that I could not find the answer to on the DESeq2 vignettes page or previous forum posts: After running res <- results(dds) and summary(res), the code says I have 8…

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Team identifies a nutrient that cancer cells crave

Arginine codons and residues are frequently lost and are associated with an increase in ASS1 expression. (A) Heatmap depicting codons gained (red) and lost (blue) across the TCGA. Gains and losses are normalized to the total number of missense and silent mutation events per sample for each cancer type. (B)…

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Molecular characterization of human cytomegalovirus infection with single-cell transcriptomics

Ethics statement All fresh peripheral blood samples were obtained after approval of protocols by the Weizmann Institutional Review Board (IRB application 92-1) and following informed consent from the donors. The study using BAL fluid samples was approved by the Hadassah Medical Organization research ethics committee in accordance with the Declaration…

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Microbially produced vitamin B12 contributes to the lipid-lowering effect of silymarin

Animals As female mice/rats resist to HFD-induced obesity and NAFLD, male mice/rats were used to induce obesity and NAFLD model by HFD50. Male Wistar (~180 g body weight; 8 weeks old) rats were purchased from Shandong Laboratory Animal Center with the permission number of SCXK 2014–0007 and raised under thermoneutral housing…

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Scientist II, Bioinformatics Job Opening in South Plainfield, NJ at PTC Therapeutics, Inc.

Job Posting for Scientist II, Bioinformatics at PTC Therapeutics, Inc. Job Description Summary: The Scientist II, Bioinformatics is responsible for planning and performing scientific experiments that contribute to PTC’s research and drug discovery activities. The Scientist II is also responsible for communicating experimental results to his/her supervisor and…

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tximeta accessing gene symbols after addIds()

Hi, I’m sure I’m missing something obvious, but is there an easy way to access the gene symbols after adding them with the addIds() function in tximeta? gse <- addIds(gse, “SYMBOL”, gene=TRUE) mcols(gse) DataFrame with 60240 rows and 3 columns gene_id <character> ENSG00000000003.15 ENSG00000000003.15 ENSG00000000005.6 ENSG00000000005.6 ENSG00000000419.12 ENSG00000000419.12 ENSG00000000457.14 ENSG00000000457.14…

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DESeq2 for small RNAseq data

DESeq2 for small RNAseq data 1 Good afternoon, I am working with a dataset containing 50 libraries of small RNAs. I am interested in all kinds of small RNAs (miRNA, tRNA fragments, piRNAs, etc.). I use an in-house script to obtain a matrix of counts: number of counts of each…

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Do I need to correct for sequencing depth in bulk RNA seq?

Do I need to correct for sequencing depth in bulk RNA seq? 1 Hello, I had 6 samples sequenced in a facility and most of them have similar amount of reads except for one that has twice as much. Do I need to do anything to correct for this? I…

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I cannot install annotables package in Rstudio (macOS)

I cannot install annotables package in Rstudio (macOS) 1 @4f002f4c Last seen 1 hour ago Canada I cannot install annotables on Rstudio. I have tried updating R to 4.2.2, it did not work on 4.2.1 or the new version. I was able to install BiocManager and several BiocManager packages using…

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DESeq2 in R 4.2.2

DESeq2 in R 4.2.2 0 @0ee98434 Last seen 17 hours ago United States I’m trying to reinstall DESeq2 with R 4.2.2. I used if (!require(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“DESeq2”) When trying to load the library, I get Loading required package: SummarizedExperiment Error: package or namespace load failed for ‘SummarizedExperiment’…

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Annelid functional genomics reveal the origins of bilaterian life cycles

Hall, B. K. & Wake, M. H. in The Origin and Evolution of Larval Forms (eds Hall, B. K. & Wake, M. H.) 1–19 (Academic Press, 1999). Nielsen, C. Animal phylogeny in the light of the trochaea theory. Biol. J. Linn. Soc. 25, 243–299 (2008). Article  Google Scholar  Garstang, W….

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Design for DE analysis in tidybulk

Design for DE analysis in tidybulk 1 @2df64073 Last seen 5 hours ago India Hi everyone, I have 12 samples – 3 Controls, 3 T1 , 3 T2 and 3 T3. I am interested in looking at genes that are different between controls and treatment. Also I would like to…

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RNA-seq library size – significant sample discrepency

RNA-seq library size – significant sample discrepency 2 Hello, I’ve been given some data to perform differential expression on, and it the process of QCing the resultant count data, I’m seeing that the library sizes have pretty big discrepancies between the 2 samples shown below. I know a good run…

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BULK mRNA-seq with UMIs. Do I need to normalize by gene length?

Hi, I am analyzed some BULK mRNA-seq data that included UMIs during the sequencing. I don’t have much experience analyzing bulk RNA-seq, and it is my first time dealing with UMIs there. I have more experience in single-cell RNA-seq, and I thought that the concept of UMIs will translate directly…

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Hugely different results between edgeR and DESeq2

Hugely different results between edgeR and DESeq2 0 I am working on a 18-patients dataset. I am trying to calculate DE genes with both EdgeR and DESeq2 for further analyses. Its a 2-factor design (Status, Fraction). I want to calculate DE genes of different Fractions using the Status as covariate….

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nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs | BMC Bioinformatics

Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci. 1976;73(11):3852–6. doi.org/10.1073/pnas.73.11.3852. Article  CAS  Google Scholar  Arnberg AC, Van Ommen G-JB, Grivell LA, Van Bruggen EFJ, Borst P. Some yeast mitochondrial RNAs…

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How to use spike-in information (sequences from another species) with DESeq2::DESeq()

Hi, I am working with colleagues to perform differential expression analyses using data that have been spiked with RNA from another species, the purpose of which is to get a sense of the absolute numbers of transcripts that are up and down between conditions. We add the spike-in at the…

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Strange results from Diffbind-Deseq2 differential peak binding of cfChip-seq with blocking

Strange results from Diffbind-Deseq2 differential peak binding of cfChip-seq with blocking 1 Hi All, I am working on cfChip-seq with the goal of comparing differentially bound peaks between two timepoints. Please note that same patients (n = 9) donated samples on the two occasions. Our quick PCA analysis showed a…

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I am running DEseq2 for single cell data transcriptomics in multicore mode. Since my last Rstudio and R update, the multicore does not work anymore

I get this error: Error in h(simpleError(msg, call)) : error in evaluating the argument ‘args’ in selecting a method for function ‘do.call’: wrong args for environment subassignment AND in my Mac’s activity manager, there is the number of cores that I wanted to use for the calculation, and they hang….

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Subset count data in DGEList using edgeR/DESeq2

Subset count data in DGEList using edgeR/DESeq2 1 @0f752196 Last seen 1 day ago United Kingdom Hello, I have an enormous methylation dataset (12.6Gb) that is proving too much for my computer to handle. This data is loaded in to R as a DGEList (with counts, samples, genes and a…

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Predicting severity in COVID-19 disease using sepsis blood gene expression signatures

Mechanisms of sepsis severity and mortality in COVID-19 patients To identify COVID-19 specific severity mechanisms, we initially compared the whole blood gene expression profiles associated with defined severity groups from a cohort of 124 patients recruited at various times relative to hospital admission. Patient severity was assessed using two measures,…

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Extracting DEseq2 results ?resultnames

Dear Community, I am using the DEseq2 package to analyze my time series data, and referring this vignet (master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments ) In brief, the dataset has two groups OP50 (control group) and SC20 (test group), harvested at 7 different time points. we are interested in DE genes in SC20 compared to…

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Help for RNA sequencing analysis with DESEQ2

Help for RNA sequencing analysis with DESEQ2 0 @80066fff Last seen 1 day ago Canada Hello everyone, I’m currently trying to perform DESEQ2 with my own RNA sequencing results. I performed whole transcriptome RNA sequencing and the subsequent analysis I performed via galaxy. I performed first fastp on the samples,…

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Bulk RNA seq with deseq2, rnaseqGene, or edgeR

Bulk RNA seq with deseq2, rnaseqGene, or edgeR 0 @fdd03415 Last seen 1 day ago United States Hi, This might be a very simple question but I am new to bulkRNAseq and would like to analyze paired FastQ files with DESeq2, rnaseqGene, or edgeR. Could anyone provide me with some…

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Manually calculating log2 fold change values from DESeq2 normalized counts

Manually calculating log2 fold change values from DESeq2 normalized counts 1 I need to calculate log2 fold change values for lot of different experimental conditions when compared to their corresponding controls. Just to mention, I am not going to use these for differential expression analysis but for some other downstream…

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Normalizing Salmon output count data matrix using DESeq2

Normalizing Salmon output count data matrix using DESeq2 1 @7cabb0d9 Last seen 12 hours ago United States I import counts and abundance matrix from Salmon output using tximport. I want to normalize the Salmon output count matrix using DESeq2 package. What code should I use to achieve this task? Can…

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Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs

Ellis, E. C. et al. Anthropogenic transformation of the biomes, 1700 to 2000. Glob. Ecol. Biogeogr. 19(5), 589–606 (2010). Google Scholar  Soleimani, T., Hermesch, S. & Gilbert, H. Economic and environmental assessments of combined genetics and nutrition optimization strategies to improve the efficiency of sustainable pork production. J. Anim. Sci….

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DeSeq2 and GenomicRange installation possible conflict with bioconductor version 3.16?

Enter the body of text here I’ve tried to install DeSeq2. and received the following warnings as shown below Code should be placed in three backticks as shown below “`Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.1 (2022-06-23) Installing package(s) ‘DESeq2’ Warning: unable to access index for repository www.stats.ox.ac.uk/pub/RWin/bin/macosx/contrib/4.2: cannot open…

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Analyzing time-series RNA-seq data using DEseq2

Analyzing time-series RNA-seq data using DEseq2 1 Hello everyone, I need a direction in using DEseq2. my Input : I have RNAseq data from two groups of mice (groups based on type of bacterial treatment). Each group was harvested at 7 different time points. In other words I have two…

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Using DESeq2 for time-series analysis with two conditions

I performing a Time-series experiment with several patients with 2 conditions and 2 time-points from each patient. The patients associated to the first condition are different respect to the second one. The experiment consist of 24 patients, 12 of them who respond to one treatment and the other 12 who…

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Accounting for differential abundance in differential expression in scRNAseq

Let’s imagine a single cell experiment in which we have 3 biological replicates, treated (TR) and untreated (UNT). After all the necessary filtering and integration steps, we isolate a cluster of interest (cluster X), for which we want to test differential gene expression (DE) between TR and UNT. Ideally one…

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Add microRNA annotation to DEseq2

Add microRNA annotation to DEseq2 0 Hello, I am trying to perform micro-RNA analysis and convert ENSEMBL IDs to microRNA I tried using Biomart and results are attached. It doesn’t produce any micro-RNA. Why is this happening and is there any other way to annotate micro-RNA into the pipeline like…

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Differentially expression analysis of orthologous genes between two species

Differentially expression analysis of orthologous genes between two species 1 @4dbfec5b Last seen 10 hours ago Netherlands Hi people, I want to use DESeq2 for differentially expression analysis of orthologous genes between two different species. I am not experienced at all using R and DESeq2, but I think at the…

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why do i get much more significant genes and wierd volcano plot with DESeq2 for my RNAseq dataand LRT not with Walds test

I’m looking into the differentially expressed genes in heat-stressed animals versus normal ones. I have a data matrix of 40 samples of different conditions and using contrast I compare each one to its the control. I want to look at the heat stressed the other 3 are non-stressed old versus…

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Assessing spermatozoal small ribonucleic acids and their relationship to blastocyst development in idiopathic infertile males

Vander, B. M. & Wyns, C. Fertility and infertility: Definition and epidemiology. Clin. Biochem. 62, (2018). Sun, H. et al. Global, regional, and national prevalence and disability-adjusted life-years for infertility in 195 countries and territories, 1990–2017: Results from a global burden of disease study, 2017. Aging 11, 10952 (2019). Article …

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Higher Dimensional RNASeq Clustering Significance

Higher Dimensional RNASeq Clustering Significance 0 @73ef4518 Last seen 29 minutes ago United States Looking at the principal components of our RNASeq data, there is clear separation between the diseased and controlled, however, this separation is in the 5th principal component, which only accounts for 0.45% of variance. There is…

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Error in DESeqDataSetFromHTSeqCount

I am using HTseq pipeline for DESeq2: Directory = “/Users/abhaykanodia/Desktop/smallRNA/” condition = c(“WT1”, “WT2”, “WT3”, “NTC1”, “NTC2”, “NTC3) sampleFiles= c(“AK1a_counts.txt”,”AK2a_counts.txt”,”AK3a_counts.txt”,” AK4a_counts.txt”,”AK5a_counts.txt”,”AK6a_counts.txt”) sampleName = c(“AK1”, “AK2”, “AK3”, “AK4”, “AK5”, “AK6”) sampleTable <- data.frame(sampleName = sampleName, fileName = sampleFiles, condition = condition) sampleTable The output is: sampleName fileName condition 1 AK1 AK1a_counts.txt…

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How to check gene properties (eg GC, repetitiveness, average expression level)?

How to check gene properties (eg GC, repetitiveness, average expression level)? 0 Hello, I am trying to compare the data from 2 sequencing machines. I aligned my data with Kallisto and then I performed DESeq2 like I normally do. I was checking to see if I was getting similar results…

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Extra-hematopoietic immunomodulatory role of the guanine-exchange factor DOCK2

Cell isolation, reprogramming and culture Approval was obtained for human cell and tissue sample collection and genetic reprogramming from the Institutional Review Board (protocols 19–252, 18–243, 21–060, 19–284 and 415-E/1776/4-2014, Ethics Committee of the province of Salzburg). Adult samples were collected in accordance with the Declaration of Helsinki after written…

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normalization of ChIP-seq data by using the spike-ins or by using total library sizes

Dear all, This question may have been asked before, I have searched the mailing list and I can not find an answer. The question is about the correct way of setting the SizeFactors() in DESeq2 in 3 situations. I would like to double check with you. Although the R code…

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Interpreting time-series analysis with DESeq2 output

Interpreting time-series analysis with DESeq2 output 1 Hello all, I read and followed time course experiment mentioned in DESeq2 vignette bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments Please see attached figure which was generated with this model: LRT p-value: ‘~ strain + minute + strain:minute’ vs ‘~ strain + minute’ I have also generated a similar…

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Quantifying Peak Height Difference in ATAC-seq

Quantifying Peak Height Difference in ATAC-seq 1 Hi, everyone. How would I go about quantifying the peak height difference of a particular gene between two a wild type and a mutant in ATAC-seq? A colleague mentioned possibly calculating a moving average of read depths for smoothing and then comparing the…

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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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Phenotypic plasticity and genetic control in colorectal cancer evolution

Sample preparation and sequencing The method of sample collection and processing is described in a companion article (ref. 23). Sequencing and basic bioinformatic processing of DNA-, RNA- and ATAC-seq data are included there as well. Gene expression normalization and filtering The number of non-ribosomal protein-coding genes on the 23 canonical chromosome pairs…

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DESeq2 design formula considerations

nhaus – This question has been asked many times both here as well as on other fora, for instance the bioconductor forum. Mike Love (the author of the DESeq2 software) has probably answered this question 50-60 times, if I had to guess, so you can find a lot on this…

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drug sensitivity prediction

drug sensitivity prediction 0 Dear all, I have been working on OncoPredict. I was able to reproduce results of calcPhenotype() using the example data. But i am bit confused with the input data. What are column and rows in each datasets used trainingExprData, trainingPtype and testExprData I have data downloaded…

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r – Cannot install bioconductor DESeq2 package on M1 mac … any advice?

This is where the installation failed. I tried installing DESeq2 on “R Studio Cloud” and it worked. I am assuming this is a mac issue. If anyone knows what to do I would very much appreciate it! Very new to R so anything will help. make: /opt/R/arm64/bin/gfortran: No such file…

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Comprehensive Analysis of NPSR1-AS1 as a Novel Diagnostic and Prognostic Biomarker Involved in Immune Infiltrates in Lung Adenocarcinoma

The incidence of lung adenocarcinoma (LUAD), the most common subtype of lung cancer, continues to make lung cancer the largest cause of cancer-related deaths worldwide. Long noncoding RNAs (lncRNAs) have been shown to have a significant role in both the onset and progression of lung cancer. In this study, we…

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Combine scRNAseq data for bulk analysis using DESeq2

Combine scRNAseq data for bulk analysis using DESeq2 0 @evocanres-17914 Last seen 2 hours ago United States I have scRNAseq data from Fluidigm C1 platform, but I have low number of cells (sample 1 ~30, sample 2 ~ 20). Can I merge the fastq files for each samples and treat…

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Opposing roles of hepatic stellate cell subpopulations in hepatocarcinogenesis

Villanueva, A. Hepatocellular carcinoma. N. Engl. J. Med. 380, 1450–1462 (2019). CAS  PubMed  Article  Google Scholar  Affo, S., Yu, L. X. & Schwabe, R. F. The role of cancer-associated fibroblasts and fibrosis in liver cancer. Annu. Rev. Pathol. 12, 153–186 (2017). CAS  PubMed  Article  Google Scholar  Mederacke, I. et al….

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Deseq2 Output Explained With Code Examples

Deseq2 Output Explained With Code Examples In this session, we are going to try to solve the Deseq2 Output Explained puzzle by using the computer language. The code that follows serves as an illustration of this point. Column Description 1 Gene Identifiers 2 mean normalised counts, averaged over all samples…

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DESeq2. Multi-factor Interactions designs

DESeq2. Multi-factor Interactions designs 0 Dear all, I want to get your feedback, please !! I have gene expression data from two tissue(Tissue_1 and Tissue_2) in three conditions(A, B and C). I want to get genes upregulated in Tissue_2 in condition C vs A+B. I was trying this, but not…

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Same results in Limma Toptable as in DESEQ2 results

Same results in Limma Toptable as in DESEQ2 results 1 Dear all, I am trying to generate exactly the same results in Limma for my result table as I did in DESEQ2 (Differential Expression Analysis). With the toptable function I am not getting lfcSE and basemean. Can anyone help me…

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Multiple conditions DESeq2

Multiple conditions DESeq2 1 Hi, I am working on differentially expressed genes analysis of RNA-seq data extracted from multiple but related experiments: experiment DESH21_E DESH40_S DESN21_E DESN21_S DESN40_E DESN40_S ES21_E ES21_S ES40_E ES40_S where, DES and ES are different in vitro cells; 21/40 are concentration (low/high), and H/N are additional…

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deseq2 – Creating multiple phenotype datasets using bootstrap method “Bootstrap-samples-by-column-of-a-data-frame-in-r” for DEG analysis

I am working on a datasets and after some discussion with my group, we doubt that maybe one or more of our controls are different than the other controls. The motivation is to see if one or more controls have been effected differently by the solvent they were kept in….

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Exporting DESeq2 results to CSV files

Exporting DESeq2 results to CSV files 1 Hello there. I need a help with this situation. I’m following this vignette and I’m getting an error on the item “Exporting results to CSV files”: write.csv(as.data.frame(resOrdered), file=”condition_treated_results.csv”) In my case i get this: write.csv(as.data.frame(resOrdered), file = “myres_counts.csv”) error in evaluating the argument…

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Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

Darwin, C. On the Origin of Species by Means of Natural Selection (John Murray, 1859). Owen, R. On the Archetype and Homologies of the Vertebrate Skeleton (Richard and John E. Taylor, 1848). Stern, D. L. & Orgogozo, V. Is genetic evolution predictable? Science 323, 746–751 (2009). CAS  PubMed  PubMed Central …

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Log2FC values slightly higher in some genes after DESeq2 shrinkage

Hi, I have a question about DESeq2 LFCshrinkage: Is it possible that some genes have a slightly higher LFC after shrinkage? It happened during my RNAseq DE analysis, I have very deeply sequenced samples with large base means. I tried visualizing using MAplot check, and it looks fine. I’m mainly…

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NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis

NDX is a heterochromatin-associated factor To understand the genome-wide regulatory roles of NDX, we first analyzed its genomic distribution. For this, we performed chromatin immunoprecipitation sequencing (ChIP-seq) in 10-day old Arabidopsis seedlings expressing N-terminally and C-terminally tagged NDX fusion proteins (flag-NDX/ndx1-1(FRI)/flc-2 and NDX-GFP/ndx1-1(FRI)/flc-2, respectively) expressed from their endogenous promoter21,32. The…

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Long non-coding RNA SNHG6 couples cholesterol sensing with mTORC1 activation in hepatocellular carcinoma

Chu, B. B. et al. Cholesterol transport through lysosome-peroxisome membrane contacts. Cell 161, 291–306 (2015). CAS  Article  Google Scholar  Luo, J., Yang, H. & Song, B. L. Mechanisms and regulation of cholesterol homeostasis. Nat. Rev. Mol. Cell Biol. 21, 225–245 (2020). CAS  Article  Google Scholar  Luo, J., Jiang, L., Yang,…

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Time course RNA seq with DESEq2

Hi all, Hope you are well. I am running time course experiment to examine differentially expressed genes from tumour tissues between two conditions, radiotherapy and sham-radiotherpapy groups at 4 time points post radiotherapy. Each time point had size matched untreated controls. I used the following code to run model with…

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TPM normalization starting with read counts

Hello everyone I have multiple bulk RNA-seq datasets that I need to apply the same pipe line on. I want to normalize them from counts data to TPM. In all datasets, I have the genes as rows, and samples as columns. Unfortunately, I don’t have the fastq files, all I…

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Feature selection for a binary classifier using mixed cancer type samples

Feature selection for a binary classifier using mixed cancer type samples 0 Hi all, I am not an expert in machine learning (ML) and have a few specific questions regarding the design of a binary classifier. I have bulk RNA-seq data for the samples from 6 different cancer types. These…

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Targeted inhibition of ubiquitin signaling reverses metabolic reprogramming and suppresses glioblastoma growth

Cell culture Human glioblastoma cells (U87MG and U87MG-Luc) and human embryonic kidney cells (HEK293) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco™ Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2 mM l-glutamine, 50 U/ml…

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I have a query regarding differential gene expression using limma-voom.

I have a query regarding differential gene expression using limma-voom. 1 @28946033 Last seen 1 day ago India I used the following pipeline for RNA Seq Analysis Fastq-Trimmomatic- Hisat2(gtf file was annotated)-featurecounts After featurecounts I tried to do limmavoom, but I get error saying this An error occurred with this…

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DESeq2 aggregated single cell data

Hi, Im aiming to use aggregated single cell data to perform a pseudobulk analysis to assess differential expression between those with sarcopenia and those without, termed “status_binary” with the levels “yes” and “no”. # DESeq2 —————————————————————— dds <- DESeqDataSetFromMatrix(y$counts, colData = y$samples, design = ~Sex+age_scaled+status_binary) # Transform counts for data…

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Batch effect correction in 2 conditions + 2 genotypes + interaction term design

Dear all, I am analyzing RNAseq data with DESeq2 for a dataset that resemble the type “2 conditions, 2 genotypes and interaction term”; specifically I have healthy donors and patients for both male and female population. I am interested in obtaining: 1- genes modulated in male patients as compared to…

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DESeq2 analysis has not been run for this contrast

DESeq2 analysis has not been run for this contrast 1 @e16bdcce Last seen 10 hours ago Hong Kong error :DESeq2 analysis has not been run for this contrast DB.DESeq2 = 0 I think until this step everything is ok here is my file↓ here is my code ↓ # dbObj_contrast…

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lncRNA analysis tutorial

lncRNA analysis tutorial 2 hello, I would like to ask if there is some good tutorial concerning analysis of lncRNA along RNAseq analysis? like practical example. thank you for your help. lncRNA RNA-seq • 458 views Generally speaking, doing differential expression (DE) or transcript discovery on lncRNA is no different…

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Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (0,2 and 4h) with 3 group (1 control, 2 treated)

Dear Experts, I have RNAseq data from 6 different plant samples (2 control, 2 Sensitive, and 2 tolerance), and different location of one species. I am trying to see the effect of the different groups at different time points, but after going through all the posts and vignettes I am…

Continue Reading Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (0,2 and 4h) with 3 group (1 control, 2 treated)

Hisat2 – stringtie – deseq2 pipeline for bulk RNA seq

Software official website : Hisat2: Manual | HISAT2 StringTie:StringTie article :Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown | Nature Protocols It is recommended to watch the nanny level tutorial : 1. RNA-seq : Hisat2+Stringtie+DESeq2 – Hengnuo Xinzhi 2. RNA-seq use hisat2、stringtie、DESeq2 analysis – Simple books Basic usage…

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Getting the best of RNA-Seq

Forum:Getting the best of RNA-Seq 0 This is not a banal discussion. I am facing some problems with the analysis of DE genes in mouse. Most methods of analysis of DE genes must face two considerations or challenges. The first needs to take into consideration the existence and the different…

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Difference in number of DEGs from Deseq2 and limma-voom

Difference in number of DEGs from Deseq2 and limma-voom 0 Hello, I have RNA-seq data from two different treatment groups (F and NF ) at 2 different time points (T1 and T2). The mapping was done with STAR aligner and the quantification was done with FeatureCounts. I run differential expression…

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Multiple disease condition vs Normal

DESeq2: Multiple disease condition vs Normal 0 Hello! I have an mRNA dataset with one cell type and 3 different conditions (Metastatic, Primary Tumor, and Solid Tissue Normal). I would like to compare the two diseased conditions with the normal. I am using the following code but getting the understated…

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Multifactor analysis

Multifactor analysis 1 @66dd6104 Last seen 1 day ago United States HI every one I am new to RNA seq analyisis using R. I Am usig DESeq 2 for my analysis. I have four different Samples with three replicates each and I want to compare all of them with control…

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Running DESeq2 from rpy2 – Askdevz

If you open R and type: you will see that the assay function is not actually coming from DESeq2, but from its dependency which is called SummarizedExperiment: > assay standardGeneric for “assay” defined from package “SummarizedExperiment” function (x, i, withDimnames = TRUE, …) standardGeneric(“assay”) <bytecode: 0x5586a354db90> <environment: 0x5586a3535e20> Methods may…

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rna seq – R – [DESeq2] – How use TMM normalized counts (from EdgeR) in inputs for DESeq2?

I have several RNAseq samples, from different experimental conditions. After sequencing, and alignment to reference genome, I merged the raw counts to get a dataframe that looks like this: > df_merge T0 DJ21 DJ24 DJ29 DJ32 Rec2 Rec6 Rec9 G10 421 200 350 288 284 198 314 165 G1000 17208…

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DESeq2 and WGCNA

DESeq2 and WGCNA 0 I am currently performing an RNAseq analysis with a dataset from a GeneAtlas where I’ve identified DEGs from different comparisons. I want to now do a co-expression analysis with these comparisons and was wondering if anybody had suggestions of tutorials I could be directed to. I…

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Deseq2 Multifactor Design – Design Forum

Deseq2 multifactor design – In fact, deseq2 can analyze any possible experimental design that can be expressed with fixed effects terms (multiple factors, designs with interactions, designs with continuous variables, splines, and so on are all possible). We have searched different posts in different forums and i can’t figure out…

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InteractiveComplexHeatmap on DESeq2 object with more than 2 groups

InteractiveComplexHeatmap on DESeq2 object with more than 2 groups 1 Hello all, I’m writing with the hope someone can clarify a doubt I have about the differential heatmap generated by the package InteractiveComplexHeatmap via the simple command interactivate(dds). I read the package documentation at bioconductor.org/packages/release/bioc/html/InteractiveComplexHeatmap.html, but I couldn’t find the…

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tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data | BMC Bioinformatics

tReasure (tRNA Expression Analysis Software Utilizing R for Easy use) is a graphical user interface (GUI) tool for the analysis of tRNA expression profiles from deep-sequencing data of small RNAs (small RNA-seq) using R packages. The whole analysis workflow, including the uploading of FASTQ files of small RNA-seq, quantification of…

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DESeq2 how to specify contrast to test difference of differences

I am trying to take the “difference of differences” in contrasts from two factors (sex and group). We have male and female animals (sex factor) that were untrained or trained for 1, 2, 4, or 8 weeks (group factor, i.e., “control”, “1w”, “2w”, “4w”, “8w”). I want to know the…

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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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Genes looking differential abundant are not accoring to DESeq2

Genes looking differential abundant are not accoring to DESeq2 0 I have a metagenomic dataset crossing three time points from which I have mined CAZymes and am using DESeq2 to identify differentially abundant CAZymes from using trimmed mean depth generated my CoverM (very similar to Q2Q3 contig coverage). From this…

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Extremely different results for both EdgeR and DESeq2 analysis

Extremely different results for both EdgeR and DESeq2 analysis 1 @373f98d7 Last seen 23 hours ago Singapore Dear all, Upon comparing my results for the analysis between DESeq2 and EdgeR, I have realized that the 2 results obtained after DEG analysis are extremely different from each other. The thresholds I…

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RNA interference triggers that target SARS-CoV-2 genome

Coronavirus disease 2019 (COVID-19) vaccines have played a critical role in reducing transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. However, with emerging reports of waning vaccine efficacy, there remains an urgent need to develop prophylactic measures against COVID-19. In a recent study published on the bioRxiv*…

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Can Differential Isoform expression analysis can be performed using DESeq2 package

Can Differential Isoform expression analysis can be performed using DESeq2 package 0 @03ddb485 Last seen 9 hours ago India Hello, I am want to perform differential isoform expression (DIE) analysis for RNAseq data from human. Can I use DESeq2 for this by inputting the transcript level abundance and getting differential…

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Counts from recount3 for DESeq2 analysis

Hi, As the topic title suggests, I want to use RSE objects from recount3 for differential expression analysis with DESeq2. This is an ongoing project that I took over. Looking at what has already been done, there are two points I wonder about : 1 – I found that the…

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deseq2 problem

deseq2 problem 0 Hi I am trying to draw a PCA plot with DESeq2 but somehow I cannot use DESeq2 functions. It is a really simple code i wil be pasting below. > transform <- DESeq2::rlog(eliminated_data, blind = TRUE) Error in (function (classes, fdef, mtable) : unable to find an…

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scrnaseq – Normalization methods to combine scRNA-seq experiments with different sequencing depths

I don’t think you need to complicate the idea of normalisation by introducing machine learning classifiers as a necessary component. Normalisation is common when comparing different datasets for all differential analysis. If you have single cell data, have a look at integration techniques in the Seurat workflows: satijalab.org/seurat/articles/integration_rpca.html If you’ve…

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DESEQ2 Results log2fold and pvalue changes after removing genes

DESEQ2 Results log2fold and pvalue changes after removing genes 1 @bine-23912 Last seen 9 hours ago UK Dear all, we have been discussing internally but couldnt find an answer, maybe you could help us. The following happened: I run my DESEQ2 analysis with the full dataset and got genes with…

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different results between DESeq model with multiple groups or with specific groups

different results between DESeq model with multiple groups or with specific groups 1 @b295d7f1 Last seen 3 hours ago Italy Hi! I am working with DESeq2 to perform a differential expression analysis between different treatments.I have 4 conditions and 4 four biological replicates for each conditions. I’ve performed differential expression…

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Tximport in usegalaxy

Tximport in usegalaxy 0 Devon Ryan: Please help in resolving this issue. How to use tximport in usegalaxy to convert transcript ID(DESEQ2-SALMON) to gene ID. I want to get gene ids from the results of deseq2(salmon) . Which GTF should be used for tximport. Iam getting the following error in…

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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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How to merge miRDeep2 counts for DeSeq2 analysis?

How to merge miRDeep2 counts for DeSeq2 analysis? 0 Hi, I am trying to identify DE miRNAs using small RNA-Seq data. I ran miRDeep2 tools mapper.pl an also miRDeep2.pl scripts and got counts for my cases. How can I merge count.cvs files of multiple cases for DE miRNA detection using…

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