Tag: deseq2

Biostar DESEQ2

Showing : DESEQ2 • reset 2 days ago • updated 1 day ago adR ▴ 10 10 days ago • updated 8 days ago adeler001 • 0 15 days ago • updated 9 days ago Cheryl • 0 updated 17 days ago by swbarnes2 ▴ 920 • written 18 days…

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Treat time variable as continuous or discrete?

Hello, I have two questions regarding an RNA-seq experiment with 10 time points and 20 replicates per time point. So far I’ve run an LRT using the following models: design = ~ timepoint reduced = ~ 1 Throughout the experiment, RNA was extracted at days 3, 4, 15, 16, 44,…

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DESeq2 input file from featureCount

DESeq2 input file from featureCount 0 Hello. I am analysing RNA-Seq data for 8 samples (2 treatments, 4 repetition each). I just finished the gene count using featureCount (Subread). How do I generate a matrix to use on DeSeq2 from the files (.RDS) genereted from featureCount? Do I just create…

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Is it not possible to use LFCshrink on the “intersect” coefficient?

Is it not possible to use LFCshrink on the “intersect” coefficient? 0 I have been trying to use the LFCshrink function on the intersect coefficient. I thought this would be possible on any coefficents from resultsNames() but it gives an error: Error in apeglm::apeglm(Y = Y, x = design, log.lik…

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normalizing EXOM-seq read using DESeq2

normalizing EXOM-seq read using DESeq2 0 @do-it-23093 Last seen 9 hours ago Germany, München Hi, I have exom read aligned to hg38. I used featureCounts to quantify the reads. Therefore, I would like to normalize the reads in the different sample using DESeq2. May I know if there especial consideration…

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just trying to launching my DE-seq2 by csv but isn’t work…

hello sir, im korean and currently work in dpt, bioenginearing… first of all, my major is basically experiment and im suddenly transferred into Industry-University Cooperation Foundation. its my first time coding r script. so i have to run DE-seq2 so that make my MA-plot(and have no idea any of r…

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no DE genes found in subset

Troubleshooting DESeq2 Analysis: no DE genes found in subset 1 @8e2958c3 Last seen 5 hours ago United States Hi, I’m quite new to R and DESeq2 and need some help troubleshooting! I’m working on analyzing a dataset comparing 3 groups: patients before and after a treatment against a healthy control…

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Read Counts from miRDeep2 for posterior DE analysis

Hello everyone, I would appreciate some help with my data: I’ve been analysing some NGS miRNA data in order to do Differential Expression profiling. Using the miRDeep2 program and algorithm, I’m in trouble when dealing with results to make a proper table in order to use it as input for…

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GOStats “genes being tested do not have corresponding GO terms”

Hi all, Has anyone ever had problems with the org.Hs.eg.db database not picking up any GO classifications for a list of genes? For example, I have a list of 21 genes, and when I try referencing the org.Hs.eg.db database, I get “genes being tested do not have corresponding GO terms”…

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Normalizing exonic reads and then log transforming or variance stabilising

Normalizing exonic reads and then log transforming or variance stabilising 0 @a-14337 Last seen 38 minutes ago United Kingdom Hi, I have raw counts per exon matrix and want to normalize and do a VST or log2 transform without running any differential expression (for downstream usage separate to DE), so…

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Genome sequencing of the multicellular alga Astrephomene provides insights into convergent evolution of germ-soma differentiation

1. Smith, J. M. & Száthmary, E. The Major Transitions in Evolution (Freeman, 1995). Google Scholar  2. Queller, D. C. Relatedness and the fraternal major transitions. Philos. Trans. R. Soc. Lond. B Biol. Sci. 355, 1647–1655 (2000). CAS  PubMed  PubMed Central  Google Scholar  3. Grosberg, R. K. & Strathmann, R….

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Question: DESeq2 multiple factor design

I have an experiment where I got 2 factor, the first one is the cell line, and the second one is the treatment. In this, one cell line is derived from the other, the derived cell line received a inducible gene. I then treated both cell lines with the inducer…

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Using normalised counts for pairwise gene correlation (pearson) across samples

Using normalised counts for pairwise gene correlation (pearson) across samples 0 Hi, I have carried out gene pairwise correlations between every pair of genes in my RNAseq data. I have done this with non-log transformed normalised counts generated from estimatesizefactors in DESeq2, as well as with VST counts and log2…

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Filtering Gene by mean expression

Filtering Gene by mean expression 0 Dear All, Sorry for another post. I have RNAseq data and used DESeq2 pipeline for differntially expressed genes. Now I am doing WGCNA and the author suggest to filter genes based on mean expression rather than variance. I am wondering whether anyone has ever…

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Elastic Net for RNAseq data

Elastic Net for RNAseq data 1 @1c386ab3 Last seen 1 hour ago Canada I have RNAseq results from NovaSeq and after doing some differential gene expression with DESeq2, I will like to explore the Elastic Net model to select features that differentiate my two conditions. However, I haven’t been able…

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Deseq2 model matrix error

Deseq2 model matrix error 1 I have trying to do Deseq2 analysis for mainly mutants vs controls. I have two covariates influencing the dataset – Gender and Genotype. This is how my sample annotation file looks – sample condition genotype gender SK01 mutant hr F SK02 mutant hr F SK03…

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DESeq2 – VST data

DESeq2 – VST data 1 @3a675fdc Last seen 4 hours ago United States I have been using DESeq2 package for RNA-sq data analysis and really like the VST data in log2 units. But was unsure about usage of VST data for certain analyses. Specifically, can the VST data be used…

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How to define the gene length for RPKM calculation

How to define the gene length for RPKM calculation 4 Hi guys, I would like to calculate the RPKM of my RNA seq experiment. To do this, as from the formula, I need to know the gene length. My starting point are the row reads (single end) counts resulting from:…

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Difference between two groups of conditions

Deleted:DESeq2: Difference between two groups of conditions 0 Hello. I intend to perform three contrasts including: i) mock.24h vs mock.4h; ii) S2.24h vs S2.4h and iii) the difference between these two comparisons (S2.24h vs S2.4h) – (mock.24h vs mock.4h). The design of my colData is as follows condition time group…

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Calculating gene expression dominance coefficient via DESeq2

I am interested in calculating dominance coefficients of gene expression. For this we have RNAseq data consisting of two homozygous lines (i.e. Genotype AA and BB, respectively) and of the heterozygous crosses between them (i.e. Genotype AB and BA, respectively). We have data for both sexes in each group and…

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Retrieving and interpreting specific contrast results from an interaction experiment in DESeq2

I have an experiment with 2 different groups, and several different time points (for simplicity, let’s say it is 2 time points), and I’m trying to find the best way to model both group and time effects. Note that time is a categorical variable. # in dds <- makeExampleDESeqDataSet(n=100,m=32) dds$time…

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S4Vectors, strange metadata behavior

S4Vectors, strange metadata behavior 0 @hauken_heyken-13992 Last seen 12 hours ago Bergen Is this internal logic intentional? makes no sense to me. # Goal: insert b or bmeta in index 1 of a # Will fail if metadata is of type GRangesList and length > 1. library(GenomicRanges) b <- bmeta…

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betaPrior and lfcShrink

Hi, I am using DESe2 (v 1.33.4) to compare three shade avoidance phenotype in Arabidopsis. I observed that the betaPrior in current version of DESeq2 was set to FALSE. If this is the case, we can compare C vs A and B vs A but we can’t compare C vs…

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Annotating DESeq2 Differential Expression Results

Annotating DESeq2 Differential Expression Results 1 @adeler001-21743 Last seen 11 minutes ago Canada Hello I am trying to annotate a DESeq2 significantly differentially expressed genes results table with the gene start (bp) , gene end (bp) and SNP ID info using the biomaRt package on RStudio, when I look at…

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filtering most variable genes

filtering most variable genes 1 Dear All, I am trying to filter most variable genes for my specific analysis. I have normalized count from DEseq2 attached here with row for genes and column for sample ID. I have found code chunk in Biostar with the following **data$variance= apply(data, 1, var)…

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filtering most variable genes

filtering most variable genes 1 Dear All, I am trying to filter most variable genes for my specific analysis. I have normalized count from DEseq2 attached here with row for genes and column for sample ID. I have found code chunk in Biostar with the following **data$variance= apply(data, 1, var)…

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How to get DEGs compare one sample to another?

How to get DEGs compare one sample to another? 0 I have a count matrix data (23 samples with different condition), and coldata is shown above. I want to get DEGS like this: I tried this code: # Read data data_matrix <- read.csv(“matrix_data”, row.names=1) coldata <- read.csv(“data/coldata.csv”, row.names=1) # Creating…

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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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Which interactions terms to choose?

Which interactions terms to choose? 0 I would appreciate your help with choosing the right structure of result names to answer my research question. I defined 2 conditions: Strain (WT is the reference level) cell-Fraction (FractionA is the reference level) I want to calculate the difference between FractionA and FractionB…

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Which rlog should I use for DESeq2 analysis

Which rlog should I use for DESeq2 analysis 0 @rafaelsolersanblas-22935 Last seen 1 minute ago Alicante I have a question regarding the rlog normalization. I have many samples to compare, with only one factor. A vs Treat, B vs Treat, C vs Treat … So, should I put everything in…

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DEseq2 contrast in two time points

I need help with some clarifications please I have control versus treatment in two time points like > y X condition time 1 CTRL_24_hrs_replicate1 control 24 2 CTRL_24_hrs_replicate2 control 24 3 CTRL_24_hrs_replicate3 control 24 4 treatment_24_hrs_replicate1 t 24 5 treatment_24_hrs_replicate2 t 24 6 treatment_24_hrs_replicate3 t 24 7 CTRL_48_hrs_replicate1 control 48…

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DEseq2 contrast in two time points

I need help with some clarifications please I have control versus treatment in two time points like > y X condition time 1 CTRL_24_hrs_replicate1 control 24 2 CTRL_24_hrs_replicate2 control 24 3 CTRL_24_hrs_replicate3 control 24 4 treatment_24_hrs_replicate1 t 24 5 treatment_24_hrs_replicate2 t 24 6 treatment_24_hrs_replicate3 t 24 7 CTRL_48_hrs_replicate1 control 48…

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Principal Component Analysis Rna Seq

Listing Results Principal component analysis rna seq Genomatix Principal Component Analysis For RNASeq Data Preview 2 hours agoThis is explained in detail on “RNA–Seq workflow: gene-level exploratory analysis and differential expression”. The matrix of raw counts is input to the DESeq2 rlog function and the resulting transformed matrix is used…

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95% confidence intervals for PCA in DESEQ2

95% confidence intervals for PCA in DESEQ2 2 @add481ab Last seen 1 hour ago United States Dear Help, We have used your package DESEQ2 (including the vst transform) on some RNA-seq data, in order to perform PCA analysis. We were hoping to add Monte-Carlo noise to the data in order…

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

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

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

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

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Bioconductor – IHWpaper

DOI: 10.18129/B9.bioc.IHWpaper     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see IHWpaper. Reproduce figures in IHW paper Bioconductor version: 3.11 This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (www.nature.com/articles/nmeth.3885) and the latest arXiv preprint available…

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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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how to extract normalized expression from DESeq2 object (dds)?

how to extract normalized expression from DESeq2 object (dds)? 1 Hi I have multiple groups to compare using DESeq2 and used contrast argument in results function to find DE. But now i would like to extract the normalized expression based on compared group for the heatmap and the further merging…

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Gene list for GO enrichment after DESeq2. Should I use a gene list of differentially expressed genes (DEG) before or after shrinkage?

Gene list for GO enrichment after DESeq2. Should I use a gene list of differentially expressed genes (DEG) before or after shrinkage? 0 Hi, I have been starting by first steps into RNA-Seq data and I have been performing my first analysis since two months ago. So I apologise if…

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DESeq2 log2Foldchange issue

Hi, when I got my DESeq2 analysis result, I found the log2Foldchange values are between -1 to 1. But when I checked the normalized read counts, I found they are hugely different between my two types of tissue (3 replicates for each type). Is that normal? My code is like:…

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Complex Contrast in DESeq2

Hi, I am using DESeq2 to look at the effect of different diet over time. I have 3 different diet (D1, D2, D3), and 3 time points (T1, T2, T3). I am trying to create best model for this, therefore I tried dds <- DESeqDataSetFromMatrix(countData=rawCounts_totat, colData=mapping_file, design=~Diet+Time+Diet:Time) dds.1 <- DESeq(dds,…

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how to combine counts and DESeq data into one CSV?

Noob question: how to combine counts and DESeq data into one CSV? 2 I am trying to replicate the format of the below file, which seems to include both the raw counts AND the DESeq data into one csv WTS1 WTS2 KOS1 KOS2 baseMean log2FoldChange lfcSE stat pvalue padj Gm6166…

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Getting samples.txt to use in the salmon to DESeq2 pipeline

Getting samples.txt to use in the salmon to DESeq2 pipeline 0 Hi all, I’d appreciate some help on the salmon-to-DESeq2 pipeline outlined here. It seems to require a samples.txt file, which I don’t have anywhere. I used Salmon to quantify my assembled transcripts (40 x 3 = 120 quant.sf files),…

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Assessment of CircRNA Expression Profiles and Potential Functions in Brown Adipogenesis

doi: 10.3389/fgene.2021.769690. eCollection 2021. Affiliations Expand Affiliations 1 Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang, China. 2 Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China. 3 Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang,…

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collapseReplicates in DESeq2 when the number of technical replicates per biosample is different

collapseReplicates in DESeq2 when the number of technical replicates per biosample is different 0 Good afternoon, I have a question about using collapseReplicates in DESeq2. As far as I understand, this function adds up the counts belonging to one biosample. I understand the meaning of this if the number of…

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Bioconductor – zinbwave

DOI: 10.18129/B9.bioc.zinbwave     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see zinbwave. Zero-Inflated Negative Binomial Model for RNA-Seq Data Bioconductor version: 3.12 Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell…

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Differentail expression analysis between 3 groups

Differentail expression analysis between 3 groups 0 Hi, I have a question on differential expression analysis. I have 3 groups(A, B, C) and each group has 20 samples. I want to do differential expression analysis to get genes differently expressed in A, not in B and C. I would appreciate…

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DESeq2 interaction terms in 2x2x2 factorial design

Hello, I’m trying to analyze RNASeq data from an multifactorial experimental setup with DESeq2. In brief, the experiment is about multiple stressor effects in stream organisms, whereby different stressors (here: added sediment, increased salinity or reduced flow velocity) are applied to the study organisms, either as single stressors or in…

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Functional profiling visualization enrichplot error: NAs introduced by coercion

Hello, I’m having trouble generating a dotplot of functionally enriched pathways across different groups. Most of them are mapped as NA via Warning message: In order(as.numeric(unique(result$Cluster))) : NAs introduced by coercion I’m trying to figure out why this happens. I’ve included the code to the original code I am adapting…

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Comparing the whole genelist by GSEA GO BP terms to adjusted pvalue genelist by DAVID GO BP terms

Comparing the whole genelist by GSEA GO BP terms to adjusted pvalue genelist by DAVID GO BP terms 0 Say I have done DESeq2 on my RNA-Seq dataset: experimental vs. control DESeq2 has a column for BH – adjusted Pvalues and I plan to take the genes with less than…

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Chapter 9 Differential abundance analysis

Here, we analyse abundances with three different methods: Wilcoxon test (CLR), DESeq2, and ANCOM-BC. All of these test statistical differences between groups. We will analyse Genus level abundances. We might want to first perform prevalence filtering to reduce the amount of multiple tests. In this particular dataset, all genera pass…

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How we can create a shiny app to run Deseq2 ? – shiny

Hello,how we can create a shiny app to run Deseq2 ?suppose i have count table and meta table as below : count_table GENE sample1 sample2 sample3 sample4 sample5 A1BG 8 8 8 7 7 A1BG-AS1 7 6 5 4 4 A1CF 6 6 6 7 6 A2M 6 6 2…

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Bioinformatics Scientist – Job at DAWSON in Bethesda, MD

Bioinformatics Scientist Full Time Prof-Entry Bethesda, MD, US DAWSON is a Native Hawaiian Organization 8(a) small business that brings the Spirit of Aloha to our employees. As part of the DAWSON “Ohana”, you will be provided a best-in-class benefits program that strives to ensure our great people have peace of…

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How to create shiny app for deseq2 object creation

How to create shiny app for deseq2 object creation 0 Hello, how we can create a shiny app to run Deseq2 ? suppose i have count table and meta table as below : count_table GENE sample1 sample2 sample3 sample4 sample5 A1BG 8 8 8 7 7 A1BG-AS1 7 6 5…

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Account for parent cell line when comparing isogenic mutants

Account for parent cell line when comparing isogenic mutants 1 @oliverziff-22402 Last seen 1 day ago United Kingdom Hi there, I am using DESeq2 to analyse RNAseq from mutants and control samples. I have 3 controls and 2 mutant samples from distinct individuals but in addition I have a sample…

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Different output when generating step by step airway dataset

rnaseqGene: Different output when generating step by step airway dataset 1 @dec8f401 Last seen 13 hours ago Spain I have been following the workflow ‘RNA-seq workflow: gene-level exploratory analysis and differential expression’ and I have a problem: I tried to generate step by step the airway dataset, downloading the fastq…

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Bug#994443: [R-pkg-team] Bug#994443: Bug#994443: marked as done (r-bioc-deseq2: autopkgtest regression)

Control: reopen -1 Hi Nilesh On Fri, 29 Oct 2021 at 21:15, Nilesh Patra <nil…@nileshpatra.info> wrote: > I think this has got nothing to do with our changes in unstable — I’d be > very surprised if so, > since essentially atleast stable is disconnected, unless some other package >…

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Help for extraction of fasta sequences

Hello everyone, I hope you are well. I am writing this post because I have a question or rather I have a problem with my workflow. Perform a workflow for RNA-seq processing as follows: quality control – Hisat2 – Stringtie – Deseq2 A simple, normal workflow that threw me important…

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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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Intersection of multiple methods for RNA-Seq differential expression: conservative or crazy?

Intersection of multiple methods for RNA-Seq differential expression: conservative or crazy? 1 Hi, For a while now, I’ve been looking at the intersect of the significant results from DESeq2 and EdgeR as my standard for determining differentially expressed genes, treating EdgeR as a filter over the DESeq2 results. I usually…

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Analyzing counts over 3 different timepoints and 2 conditions with DESeq2

I am trying to analyze data that has three different timepoints (0, 6, and 12 hr) and two conditions (treated and control), but every attempt I make to carry this out with DESeq2 is met with error. The latest is below, which is an attempt I made using this brief…

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DESeq2 Timecourse design

DESeq2 Timecourse design 0 @071d71ad Last seen 15 hours ago United States Hi all, I am interested in analyzing timecourse data but would like some advice as to the experimental design in DESeq2. The experimental data include 4 ramets of a single sapling (tree) clone collected on Day 0 (before…

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DESeq2 MA plot label subset of genes

DESeq2 MA plot label subset of genes 2 Hello, I’m new to R and I’m trying to make a MA plot from my DESeq2 results using ggplot2. I have figured out how to make a MA plot using the following code: plot_poly <- all_counts.poly.results %>% as.data.frame() %>% ggplot(aes(log2(baseMean), log2FoldChange) +…

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Generating heatmaps of pre-selected candidate genes after deseq2

Generating heatmaps of pre-selected candidate genes after deseq2 2 Hi biostars, Is it possible to make a heatmap for a preselected list of genes after deseq2 DGE analysis? I wanted to represent the log2FC of 20 differentially expressed candidate genes as a heatmap. RNA-Seq DESEq2 heatmap • 4.1k views Hi,…

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Select a list of genes of interest to visualise in heatmap of DESeq object

Select a list of genes of interest to visualise in heatmap of DESeq object 1 Hi, I have previously generated heatmaps of the top x genes in DESeq2 using the following code: topVarGenes <- head(order(rowVars(assay(rld)), decreasing = TRUE), 20) mat <- assay(rld)[ topVarGenes, ] mat <- mat – rowMeans(mat) anno…

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Mapping RNAseq counts to genomic loci

Mapping RNAseq counts to genomic loci 0 Hello. I am trying to figure out a way to map count reads from RNAseq datafiles to genomic loci and display this data in an elegant way (ideally circos plots). However, most of the tools I have come across (edgeR, DEseq2) require a…

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DESeq2 cannot relevel

Hello, Sorry, I’ve seen that this is a common problem, but for some reason none of the provided solutions has worked for me. Basicaly, I am trying to relevel, as explained in the vignete. I have CV vs control, but I want the other way around. When I get to…

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DESeq2 with multiple variable give me different results

I am doing a DESeq2 comparison with different levels and one factor. To do this, I have performed the analysis in two different ways. First, putting all the samples in the same DESeq object and then extracting each comparison: > sampleinfo FileName SampleName Status A_1_count A_1 A A_2_count A_2 A…

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DESeq2 ratio of ratios and p-value

Hello, I am new to DeSeq2 and I am trying to use a multi-factor design to answer this question: Is captured/input in condition 1 different from captured/input in condition 2 ? I used a combination of the DeSeq2 manual and DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling) to…

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Bioconductor – sparrow

DOI: 10.18129/B9.bioc.sparrow     Take command of set enrichment analyses through a unified interface Bioconductor version: Release (3.14) Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of…

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Gene expression (RNA-seq) clustering

Unsupervised class discovery is a data mining method to identify unknown possible groups (clusters) of items solely based on intrinsic features and no external variables. Basically clustering includes four steps: 1 Data preparation and Feature selection, 2 Dissimilarity matrix calculation, 3 applying clustering algorithms, 4 Assessing cluster assignment I use…

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Extracting GeneID from Dbxref section in GFF file while using featureCounts

Extracting GeneID from Dbxref section in GFF file while using featureCounts 1 Hi all, I’m trying to generate feature count files for the DeSeq2 pipeline, but I’ve run into an issue while using featureCounts . I see that the gene IDs that I need, aren’t in the same format at…

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DiffBind Issue with coordinates

I am analyzing ChIP data. I called peaks with MACS2 run through a RECAP wrapper script. I am attempting differential binding analysis using DiffBind. Code shown below. Please note I have tried the suggestion in biocondutor support from Stark (the developer) to explicitly set the datatype as part of dba.report….

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How does diffbind extract the original coordinates of each difference peak

How does diffbind extract the original coordinates of each difference peak 0 After using dba. analyze() to calculate the difference, use dba. report() to extract the difference peak, but the difference peak coordinates have been merged. How to output the real peak coordinates corresponding to each difference peak in different…

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best practice for applying FDR to highly similar group DEG analysis

hi, i am grad student who is mid of master’s degree. one of my project is revealing some genes that differentially expressed between cancer that has small size and do not lymph node metastasis and cancer that has small size and do lymph node metastasis. i’d done sampling from 10…

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DESeq2 rows did not converge in beta, how to solve

Hello! We are using DESeq2 to analyse RNAseq data from an experiment and are running into convergence errors that we are unable to solve. We are not sure what is causing these errors; and would preferably solve them rather than dropping the genes with the error from the results. We…

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AKIRIN2 controls the nuclear import of proteasomes in vertebrates

1. Johnston, L. A., Prober, D. A., Edgar, B. A., Eisenman, R. N. & Gallant, P. Drosophila myc regulates cellular growth during development. Cell 98, 779–790 (1999). CAS  PubMed  Article  Google Scholar  2. Sabo, A. et al. Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis. Nature 511,…

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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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Error in Galaxy using Deseq2 “Error in data.frame(…, check.names = FALSE) :”

Hello everyone How are things going? Currently, I am processing ARN-seq data using Galaxy. I would like to observe the differential expression between controls and cases. For that, I follow the following steps: I did a quality check of my library first (obviously) Second, I used HISAT2 for reference genome…

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error while plot data with deSeq2

error while plot data with deSeq2 0 Hi, I am getting an error while plotting figures after running DESeq2. Here is what I have done: dds <- DESeqDataSetFromMatrix(countData = mydata, colData = meta, design = ~ Diet) dds <- estimateSizeFactors(dds) dds <- DESeq(dds) plotCounts(dds, gene=”ENSSSAG00000003723″, intgroup=c(“Diet”) ) Error in .local(object,…

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DESeq2 normalization when using with derfinder

Hi, I have a question about whether I should set the sizeFactors to 1 prior to using DESeq2 on the counts obtained from derfinder. I have normalized bigwig files ( using deepTools ), which I use as input to derfinder. Following the instructions in the users guide : lcolladotor.github.io/derfinder/articles/derfinder-users-guide.html#expressed-regions-level-1 My…

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CIBERSORT input file for RNA-Seq data

CIBERSORT input file for RNA-Seq data 0 Hi, I am trying to figure out CIBERSORT for RNA-Seq data. I have 5 control samples and 32 patient samples. I have DeSeq2 outputs and count data. I have 2 questions. 1.Should I use DeSeq2 outputs as input to CIBERSORT for Impute Cell…

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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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DESeq2 installation problems

DESeq2 installation problems 0 Hello. I’m having problems installing the DESeq2 package. I keep getting this error mesage below. The downloaded source packages are in ‘C:UsersNameAppDataLocalTempRtmp67gd4pdownloaded_packages’ Warning message: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:UsersNameDocumentsRwin-library4.00LOCKxfunlibsx64xfun.dll to C:UsersNameDocumentsRwin-library4.0xfunlibsx64xfun.dll: Permission denied The commands I used were: if (!requireNamespace(“BiocManager”, quietly…

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DESeq2 input file

DESeq2 input file 1 Hello. I’m trying to analyzing RNA-seq data with DESeq2 to study differencial gene expression. I have SAM and BAM files generated by samtools. How do I insert my files on R to run DESeq2? Do I use the SAM files, BAM files or sorted BAM files?…

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Greatly speed up conda by using mamba

Conda has been my go-to software manager, but it was only recently brought to my attention that a well maintained project has aimed to greatly speed up and improve the conda functions. Mamba is an almost complete rewrite of conda in C++, allows for parallel downloading of data, and has…

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DESeq2 R markdown plotting problem

DESeq2 R markdown plotting problem 0 Hello! I’m working on my DESeq2 data analysis and I want to make a report with R Markdown. But I have a problem when I get to the deseq2 plotMA part. In the markdown HTML I get a plot like this: But when I…

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Running DEseq2 on galaxy having error for invalid row.names length

Running DEseq2 on galaxy having error for invalid row.names length 0 While running DEseq2 on Galaxy I always run into this error, and I have no idea what does it mean, the datasets have the same length and all the same structure. This job was resubmitted to the queue because…

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mitochondrial RNA percentage in bulk RNAseq data

mitochondrial RNA percentage in bulk RNAseq data 0 @335cd804 Last seen 16 hours ago United States Hi, I am analysing bulk RNAseq data of 86 samples by DESeq2. I really liked one feature of Seurat in scRNAseq analysis “mitochondrial content percentage” . Is there a simple way to extract “mt…

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Bioinformatics Scientist with Security Clearance job in Bethesda at Dawson

Company Description Dawson is a Staffing & Recruiting agency that was founded in 1946 and headquartered in Columbus, OH. They have the vision to help the small as well as large corporations and businesses to recruit the talent that can help them to provide the best customer service with exceptional…

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DESeq2 Large Log2FoldChanges but padj>0.1

DESeq2 Large Log2FoldChanges but padj>0.1 1 Hello! I want to kindly ask a question regarding DESeq2. I am getting large log2fold changes (absolute log2fold changes greater than 0.5), but the padj values are not significant (padj>0.05). However, some genes in my data have low log2fold changes (absolute log2fold changes lower…

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DESeq2 lfcshrink, normal vs. apeglm

DESeq2 lfcshrink, normal vs. apeglm 0 Hello! I want to kindly ask a question regarding the lfcshrink function of DESeq2. We realized that the log2fold changes in our data are abnormally large (above 20), so we decided to use the lfcShrink() function. However, I have been doing some reading and…

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DESeq2 Glimma2 visualisation error

I’m working on my RNA-seq pipeline, with deseq2, and I would like to use Glimma2, for interactive visualisation. My problem is that, after I do the DESeq analysation, I can’t plot it. On different sites, It is said, that it is as simple as: glimmaMA(dds) But I get the following…

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DESeq2 Design Matrix Two Conditions and Two Treatments

Hello, I kindly ask for help comparing the interactions terms between two groups. I have two groups (two conditions/types) and two treatments. the meta data is as follows sample type treatment 1 Control_ND_1 Control ND 2 Control_ND_2 Control ND 3 Control_ND_3 Control ND 4 Control_ND_4 Control ND 5 Control_D_1 Control…

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The translatome of neuronal cell bodies, dendrites, and axons

Significance Proteins are the key drivers of neuronal synaptic function. The regulation of gene expression is important for the formation and modification of synapses throughout the lifespan. The complexity of dendrites and axons imposes unique challenges for protein supply at remote locations. The discovery of messenger RNAs (mRNAs) and ribosomes…

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Contrast treated samples against both scramble and untreated controls

Hi there, I am using DESeq2 to analyse RNAseq from siRNA treated samples and 2 controls (Scramble and Untreated). Each treatment has 4 cell lines: treatment cellline group <fct> <fct> <fct> 1 Untreated 1 Control 2 Scramble 1 Control 3 Knockdown 1 Knockdown 4 Untreated 2 Control 5 Scramble 2…

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How to make tests for the RNA-Seq, proteomic, clinical data

How to make tests for the RNA-Seq, proteomic, clinical data 0 Generally, there are thousands of genes/proteins/clinical with several samples per group in the RNA-Seq or proteomic data. Should I test the normal distribution per gene per group (plan A) or using all the data (such as a matrix containing…

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non-unique values when setting ‘row.names’ error in DESeq2

non-unique values when setting ‘row.names’ error in DESeq2 0 Hi Everyone! I am trying to run the DESeqDataSetFromMatrix() command using a specific dataset but I keep getting the following error. For some reason, R (version 4.0.5) is trying to assign the first column of my DataFrame to be the row…

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My “Ask a Question” post has been flagged as spam

My “Ask a Question” post has been flagged as spam – it is not 1 @ladypurrsia-11377 Last seen 17 hours ago United States I recently posted a question under the Ask a question option. However, after posting, it was immediately flagged as spam. It is not. I really do need…

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