Tag: DESeq

DOI: 10.18129/B9.bioc.BioNERO     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see BioNERO. Biological Network Reconstruction Omnibus Bioconductor version: 3.15 BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses…

About the tool The FASTA format is a text-based format for representing nucleotide or peptide sequences. The FASTQ format additionally includes the corresponding quality scores. This tool allows you to convert FASTQ files to FASTA. The resulting FASTA file will contain only the sequence data from the input FASTQ file….

Running Deseq2 with all samples vs samples for each comparison separately 1 @52b8b937 Last seen 5 hours ago Portugal Hello, I am currently using Deseq2 to perform differential analysis on my data. I have feature count data for 24 samples and 4 comparisons to do ( for each comparison I…

Deseq2 output and robust PCA (PcaGrid and PcaHubert) 0 Hello there, I followed the deseq2 file to get the list of differentially expressed genes of a dataset I am working on. The Pca graph I got was not enough to show which one of the replicate is an outlier. A…

komal (Komalk) January 19, 2024, 12:02pm 1 Hi this is regarding DESeq2. I first created a phyloseq object from qiime2 artifacts and then subjected it to Deseq2. At one step I got a errorError in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, :every gene contains at least one zero, cannot compute log geometric…

Forgive me if this post is messy, I’m new to this! I’m analyzing RNA Seq data and found that one of my samples is an outlier (sample AV17). I’m trying to exclude it from my analysis, but whenever I do, using this code: dds = subset(countData, select = -c(AV17) ),…

Troubleshooting RNA-seq data with DNA contamination 0 Hi everyone, If there has been DNA contamination in the RNA samples and RNA-seq was conducted. After RNA-seq, I tried using SeqMonk and I estimated contamination levels, which were highly variable between samples, ranging from 1.7% to 10.5%. My initial step was to…

Quantile normalisation on RNAseq with substantial differences on sample size 0 I tried vst and rlog from DESEq2 for my RNA seq data. But i suspect the largest group (condition 1 with 60 samples) has affected the variance from other groups (condition2 with 20 samples, condition 3 and 4 with…

installing DESeq2 on Windows 0 I have a problem with installing DESeq2 on Windows. The problem started with installing libraries that DESeq2 uses so I’m installing them individually. I do it by: ‘BiocManager::install(‘zlibbioc’)’ . I got an error that suggests that is something wrong with compilation: C:\rtools43\x86_64-w64-mingw32.static.posix\bin\windres.exe: can’t popen `C:\rtools43\x86_64-w64-mingw32.static.posix\bin\gcc.exe…

Forum:LncRNA pipeline 0 HI ALL, I AM WORKING ON FINDING LNCRNA, I WOULD LIKE TO CHECK IF MY PIPELINE IS RIGHT FIRST I MAP USING STAR AND THEN SORT IT AND THEN GO FOR HTSEQ -GET THE COUNT DATA AND DO DESEQ. FOR LNCRNA EXTRACTION FROM RNA SEQ, I AM…

Hello, I’m trying to use SVA to calculate SVs in my DESeq2 analysis. In a couple of examples, I’ve seen people generate model matrices using the raw data, but actually calculate SVs on normalized data. For example, this post: Designing of model.matrix for batch correction of Time Course data ?…

Hello! I’m having issues generating an adequate geneList for running gseGO in clusterProfiler, using keytype = “GO” Similar issues have been described here: No gene mapped gseGO code is: gse <- gseGO(geneList = gene_List, ont = “ALL”, #ont one of “BP”, “MF”, “CC” or “ALL” OrgDb = OrgDb, minGSSize =…

Waters JK, Reznik SI. Update on management of squamous cell esophageal cancer. Curr Oncol Rep. 2022;24:375–85. Article  PubMed  Google Scholar  Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185…

scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts? 1 @03836aaf Last seen 5 hours ago United States Hi, I’m using AggregateExpression() function to convert my scRNA-seq data into pseudobulk for differential expression with Deseq2. I’m wondering whether AggregateExpression() simply sums the counts for each gene in each cell, or…

Hello everyone, I am an absolute beginner on sequencing analysis and DESeq2, so please forgive me for possibly mundane questions. I have tried to look up different methods, but couldn’t find a fitting answer yet. I am currently working with sequencing data derived from an Illumina sequencer. The data is…

I am working with data from an RNAseq containing expression values for about 3000 genes, including measurements from diseased and control patients. My goal is to train machine learning models, Lasso and random forest, in order to select which subset of genes is able to perform better disease prediction. I…

Hello, I am performing DGE analysis using DESeq2. I have two groups to compare: CTRL and SA, and I have performed a group comparison using DESeq2 and there’s no issue with that. However, I have males and females in each group, and I’m curious to see if there’s an interaction…

Hello all, Hope you’re well. I would really appreciate it if you take some time and give me feedback on my experimental design. It is valuable to me. I am doing single nucleus RNA sequencing and using DESeq2 package for my DE analysis. My sample information is as below: Case:…

DOI: 10.18129/B9.bioc.airway     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see airway. RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Bioconductor version: 3.15 This package provides a RangedSummarizedExperiment object of read counts in genes for…

Allam RM, Al-Abd AM, Khedr A, Sharaf OA, Nofal SM, Khalifa AE, Mosli HA, Abdel-Naim AB (2018) Fingolimod interrupts the cross talk between estrogen metabolism and sphingolipid metabolism within prostate cancer cells. Toxicol Lett 291:77–85 Article  CAS  PubMed  Google Scholar  Andrews S et al (2010) FastQC: a quality control tool…

As the title suggestions, I’m wondering what the best way to test each gene in a count matrix containing two groups is, where one group is expected to have a global increase in gene expression. I need to use spike-in normalized RPKM data, so from my understanding of DESeq, it…

downstream analysis on the output of nf-core/rnaseq pipeline 1 Hello everyone, I ran nf-core/rnaseq pipeline successfully, now I want to do downstream analysis like machine learning on the generated output files from this pipeline. Should I use salmon.merged.gene_counts.tsv for that and apply log transformation to normalize it before doing downstream…

Comment: flowCore >2.0 read.FCS results in $SPILLOVER error when reading certain FCS file by SamGG &utrif; 320 Hi. rbio2021 has no spillover, so no problem with current flowCore. As you identified it, the spillover matrix of rbio2023 has a header bu… Answer: Running DESeq on normalized data by James W….

I’ve conducted a DESeq2 analysis on a large volume of data and I’m trying to make box plots that compare the counts of specific genes, which are sorted into 2 groups, and include statistical significance. Using the plotCounts() function works fine, but I’m struggling to add the p.adj values calculated…

Hi all, I’ve come back to WGCNA after some years and have run into a bit of a quirky result when looking at my soft power thresholds depending correlation the methods I use. Generally, this topic has been discussed a fair bit – but was looking to see if anyone…

Using STAR’s readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport 1 @e0db819c Last seen 1 day ago United States Hi, I am new to RNA-seq analysis. I have finished RNA alignment using STAR, and got ReadsPerGene.out.tab outputs. I am trying to use tximport to build a gene-level…

Linear Model Fitting and Colinearity 1 @7220be07 Last seen 9 hours ago United States Hello All, I have an RNAseq experiment with paired samples (before and after treatment). For each sample, I also have metadata on the patient such as sex. The only comparison that I care about is the…

Hello everyone, I’ve been working extensively with a small RNA-seq dataset comprising 47 samples, each associated with a specific date and categorized into ‘ON’ or ‘OFF’ conditions, with three replicates per condition (except for one condition with two replicates only). This dataset encompasses the counts of 77,000 small RNA molecules…

removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…

Using Metagenome Samples for HNSCC analysis 0 So I’m trying to analyze the floor-of-mouth HNSCC(Head and Neck Squamous Cell Carcinoma) and controls. I’m going to be using SRA files. The issue I’ve encountered is that I could only find 2 controls. The 2 controls were tumor-adjacent normals. For floor-of-mouth, there…

Hi, I am hoping this isn’t a stupid question as I am really lost here. I have extensively read the manual and other forum posts but am struggling to find a solution. I am using DESeq2 to analyse my data set but running into problems with an interaction term in…

Good afternoon, I am working with a dataset of 7 patients. I have merged all raw counts to one count object with JoinLayers: Now I would like to know whether there are certain genes differentially expressed between my Seurat clusters. For that I ran markers_all<-FindAllMarkers(kid.filtered_new, test.use=”DESeq2″, slot=”counts”) However, it does…

Normalization of RNA captureSeq data (<20 genes captured) 0 Hi all Hope someone can help with this. We are working on RNA captureSeq experiments where we perform targeted RNAseq on 20 genes of interest (+ probes for the 92 ERCC standards). In the initial phase of the experiment we were…

Opinion on miRNA pipeline 0 Dear colleagues, I am currently in the process of evaluating miRNA Seq data and would like to present my pipeline for your review. Given the absence of a dedicated bioinformatician in my department, particularly for this specific use case, I am eager to gather feedback…

Differential expression using Bowtie2 0 Hi, I have a gene and I want to investigate its expression in different organs. I’m not sure how best to do this though. I am thinking of using Bowtie2 to either: Align the transcript of the gene to the transcriptome for a cell in…

Multi-factor designs in DiffBind 1 Dears, I’m trying to analyze some ChIPseq data using DiffBind. Samples has been processed in two different times SampleID Name Factor IP Condition Replicates 5 PBS_Pol2 S3 Batch1 Pol2 PBS 1 6 PBS_Pol2 S9 Batch2 Pol2 PBS 2 7 C26_Pol2 S4 Batch1 Pol2 C26 1…

Friedman-Einat, M. & Seroussi, E. Avian leptin: bird’s-eye view of the evolution of vertebrate energy-balance control. Trends Endocrinol. Metab. 30, 819–832 (2019). Article  CAS  PubMed  Google Scholar  International Chicken Genome Sequencing C. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716 (2004)….

DESeq2 : stat or lfcshrink for GSEA analysis 1 @0318a29a Last seen 19 hours ago France Hi, I see the advantage of using lfcshrink in DESeq2 analysis for getting a more “realistic” FC that takes into account the variance of the data. I have a question regarding what variable generated…

Ambient RNA removal method that generates whole (integer) counts 0 I am envisioning a project that requires removal of ambient RNA counts from cell-containing droplets. On the other hand, I will also need to aggregate counts from individual mice into “pseudobulk” profiles, to use as input to between-condition DE analysis…

DOI: 10.18129/B9.bioc.octad   This is the development version of octad; for the stable release version, see octad. Open Cancer TherApeutic Discovery (OCTAD) Bioconductor version: Development (3.19) OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene…

contrast file in DESeq2 bioconductor 1 Hi everyone, I have 3 time points and want to do deseq2 for comparing these 3 time points: is it correct to build my contrast file like below? results(dds, contrast = c(“timepoints”, “TS”,”EOT”, “FU”)) I can also take TS (Therapy start) as control and…

How does Deseq2 deal with the row with zero when calculating size factors 0 @7dbff853 Last seen 1 hour ago United States Hi, I am confused about the calculation of the size factors when the gene has at least one zero count in the samples when using the default params….

Cell line and growth assays Cell lines were grown in Roswell Park Memorial Institute-1640 medium (RPMI-1640) with 1% penicillin–streptomycin (10,000 U ml−1) and 10% FBS or in Iscove’s modified Dulbecco’s medium (IMDM) with 1% penicillin–streptomycin (10,000 U ml−1), l-glutamine (200 mM) and 10% FBS in a humidified incubator with 5% CO2 maintained at 37 °C. Drugs…

Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006). Article  ADS  PubMed  Google Scholar  Halban, P. A. et al. β-cell failure in type 2 diabetes: postulated mechanisms and prospects for prevention and treatment. Diabetes Care…

A supply of nitrate triggers organ-specific changes of histone modifications at specific gene loci To investigate the organ specificity of dynamic histone modifications in response to N changes, we treated 3-week-old tomato seedlings (Solanum lycopersicum, cultivar M82) with four days of N starvation, followed by N-supply (2.8 mM NO3−; +N) or…

Jiao, Y. N. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011). Article  PubMed  Google Scholar  Levin, D. A. Polyploidy and novelty in flowering plants. Am. Nat. 122, 1–25 (1983). Article  Google Scholar  Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of…

New BMC Bioinformatics Paper on “Transformer-based tool recommendation system in Galaxy” Abstract: Background: Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a collection of tools that can be used to extend…

Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article  ADS  CAS  Google Scholar  Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…

“Current Protocols in Molecular Biology“, 1991, JOHN WILEY & SONS, pages: 6.3.1 – 6.3.6 “Quantitative monitoring of gene expression patterns with a complementary DNA microarray.“, SCIENCE, vol. 270, no. 5235, 1995, pages 467 – 70 ALTSCHUL ET AL., J. MOL. BIOL., vol. 215, 1990, pages 403 – 410 ALTSCHUL ET…

Materials Animals All of the mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics. The mice were maintained under specific-pathogen-free conditions, with 2 to 5 mice housed in individually ventilated cages (Techniplast). The cages were equipped with bedding material, nesting material, a paper…

gene set enrichment analysis- by enrichGO 1 Hey, I ran DESeq and identified differentially expressed genes. I noticed that for running enrichment analysis, it’s recommended to select genes with a fold change bigger than 2. My question is, do I also need to filter by p-value or p-adj? Is this…

How to do KEGG pathway analysis when I have a gene with multiple entrez IDs? 0 Hello, I did DESeq2 on my samples and I have a list of DEGs that I would like to do kegg pathway analysis on. For DESeq2 I used biomart and tximport to assign external…

CHIPSEQ Analysis , DiffBind Parameters 0 Hello, Regarding Diffbind, How does diffbind calculate common peaks with the samples. I’m observing that certain peaks identified as common using bedtools intersect are not appearing in the output report file generated after DiffBind analysis Command used to write the file : res_deseq <-…

Kumar A, Rasche H, Grüning B, Backofen R. Tool recommender system in Galaxy using deep learning. GigaScience. 2021. doi.org/10.1093/gigascience/giaa152. Article  PubMed  PubMed Central  Google Scholar  The galaxy community: the galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res 50(W1):W345-W35104 2022. (2022). doi.org/10.1093/nar/gkac247 Gil Y, Ratnakar…

Generate Read counts from bam file 2 Currently i am working on a project related to LHON disease (rare mitochondrial disorder which leads to progressive visual loss). I have 9 RNA-seq fastq files out of which 3 are for carriers, 3 for affected and 3 for control. Data downloaded is…

A major problem in meta-analysis is combining p-values from different datasets, particularly in domains like genomics where high-dimensional data is frequently handled. Here’s a summary of how to use a negative binomial-generalized linear model (NB-GLM) in your case with RNA-seq data: First, individual analysis: Typically, you want to run the…

Hi all, I am new to bioinformatics analysis, so I’d appreciate if someone could check my code for the goal I am trying to achieve. I have 3 samples – Wild Type (WT) FoxP3-TCF-HEB (I have 3 replicates of this) TCFKO I have defined these in the sample information csv…

DEseq2 input 1 Hello Guys, @Michael Love I have a transcriptomics dataset and did rnaseq/nf-core pipeline by salmon-star. my output of the salmon-star folder is as follows: salmon.merged.gene_counts.tsv salmon.merged.gene_counts_length_scaled.tsv salmon.merged.gene_counts_scaled.tsv salmon.merged.gene_lengths.tsv salmon.merged.gene_tpm.tsv salmon.merged.transcript_counts.tsv salmon.merged.transcript_lengths.tsv salmon.merged.transcript_tpm.tsv tx2gene.tsv my question is: which one of these files should be an input for Deseq2…

In my experiment, I have three groups of plants: wild-type (WT), induced (IN), and uninduced (UN). These groups have been established to explore the effects of a specific gene, which I refer to as gene DM, that I can induce with ethanol (EtOH) treatment. The IN group is composed of…

Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes 0 @4b83ad99 Last seen 1 day ago Canada Hello, This question is crossposted from Biostars as I wasn’t sure which platform is the more appropriate one for asking it. I am studying the gene expression of a…

Ward, Z. J. et al. Projected U.S. state-level prevalence of adult obesity and severe obesity. N. Engl. J. Med. 381, 2440–2450 (2019). Article  PubMed  Google Scholar  Khaodhiar, L., McCowen, K. C. & Blackburn, G. L. Obesity and its comorbid conditions. Clin. Cornerstone 2, 17–31 (1999). Article  CAS  PubMed  Google Scholar …

DEseq2 : Complex design with a mixture of male and female mice 0 @2bfe541c Last seen 4 hours ago France Hello everyone, I’m working on a scientific project that poses a particular problem. The experimental design includes 3 times and 2 conditions (WT and KO). Each time*condition has 3 mice….

Mice C57BL/6N (strain 005304), C3H/HeJ (strain 000659), FVB/NJ (strain 001800), BALB/cJ (strain 000651) and NSG mice (stock 005557) were purchased from the Jackson Laboratory. CD-1 (stock 022) mice were purchased from Charles River. Mice (6–20-week-old) of each strain/background were used for teratoma assays. Mice were housed in a pathogen-free facility…

Plasmid construction All the constructs used in this study were generated with standard cloning strategies, including PCR, overlapping PCR, oligo annealing, digestion and ligation. Primers were purchased from Genewiz. The plasmid sequence was verified by Sanger sequencing. The pCAG-spike(D614G)-GFP11-mCherry plasmid was modified from Addgene plasmid 158761. Briefly, GFP11 and mCherry…

Hello, The data is related to my previous post. We decided to remove 3 genes from the sample count matrix as they were also present in negative controls in very high count. When running DESeq(dds), we got the following error – estimating size factors Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,…

Identifying differentially expressed loci for gene duplicates using DESeq2 0 Hello, I am studying the gene expression of a species that has undergone a duplication event. I have a synteny table of gene duplicates for multiple tissue types, which was derived using the genome of a related ancestral species (that…

Summary Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY,…

I have an RNAseq dataset that I want to perform differential gene-expression analysis on. The dataset consists of 3 groups = macrophages deriving from adults (n=6), term-born infants (n=5), and preterm infants (n=3). Each sample has been treated with an immune-stimulus, or left untreated (paired samples). Group Treatment Sample_Nr Sample_within_group…

Help doing differential expression analysis -experimental design and gProfiler TF interpretation- 0 Hi! I’m trying to do a differential expression analysis using breast cancer TCGA data. Firstly, I split the breast cancer cohort into two groups based on the expression level in z-score of a particular gene I’m interested in,…

DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample 1 @e3bc7671 Last seen 54 minutes ago United Kingdom Hello, This is a question related to RNAseq expression and the need to extract biologically relevant results at single patient level. For context,…

Deseq2 5 level condition – building contrast 0 Hello I need your help with my analysis. So i have an bulk Rna-seq dataset which contains data from ips cells which develop into neurons in 5 days For each time point I have 7 replicates So now with deseq2 I have…

Hello all, Background: I’ve inherited a new RNAseq data set and am thinking about updating my approaches (last time I did this I was using HISAT and Cuffdiff). I’d like some opinions on best strategies to disentangle/filter out parasite microbe reads from infected host reads before preforming a differential gene…

Krause, J. & Ruxton, G. D. Living in Groups (Oxford Univ. Press, 2002). Réale, D., Reader, S. M., Sol, D., McDougall, P. T. & Dingemanse, N. J. Integrating animal temperament within ecology and evolution. Biol. Rev. 82, 291–318 (2007). Article  PubMed  Google Scholar  Gartland, L. A., Firth, J. A., Laskowski,…

Cell growth and transfections Procyclic form (PCF) T. brucei, strain 29-1354, which carries integrated genes for the T7 polymerase and the tetracycline repressor, was grown in SDM-79 medium supplemented with 10% fetal calf serum, in the presence of 50 μg/ml hygromycin. Cells were grown in the presence of 15 μg/ml G418 for…

Introduction The CRISPR-Cas system is a widely used genome engineering technology because of its simple programmability, versatile scalability, and targeting efficiency (Wang & Doudna, 2023). Although researchers are rapidly developing CRISPR-Cas9 tools, the biggest challenge remains to overcome undesired on- and off-targeting outcomes. Previous studies have reported unintended genomic alterations,…

coupling Cufflinks results with RSEM 0 Hello! I am opening this post to ask if I can use the transcript-level assembly obtained with Cufflinks (using a reference genome) to independently quantify the abundance levels of these sequences with RSEM (transcript-level quantification), specifically designed to quantify isoforms. Subsequently, I would perform…

Three questions about datasets 2 Hello, I have three questions about Rna-seq and datasets: Is it fine to combine datasets? Suppose I am doing a project comparing control tongue epithelial tissue vs. tumor tongue epithelial tissue through DESEQ2 analysis. I have 5 control sra files from one experiment and 5…

Batch effect correction between Bulk RNA-Seq and scRNA-Seq’s clusters 1 Hello, I need to compare some samples from different bulk RNA-Seq with some clusters of a scRNA-Seq (not whole sample) to find DEGs. We have undifferentiated samples performed by bulk RNA-Seq and fully differentiated samples (mature ones) are 2-3 clusters…

Hello, I am fitting splines in DESeq2 like so: dds <- DESeqDataSetFromMatrix(countData = counts, colData = coldata, design = ~ ns(age_scaled, df = 3)) Plotting later using the code Mike Love posted elsewhere: dat <- plotCounts(dds, gene, intgroup = c(“age”, “sex”, “genotype”), returnData = TRUE) %>% mutate(logmu = design_mat %*%…

Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager)Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)BiocManager::install(“DESeq2”)‘getOption(“repos”)’ replaces Bioconductor standard repositories,…

DESeq2 installation failures 0 Help! I’m trying to install DEseq2 to perform differential gene expression analysis R Studio. I’m using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8. This is my issue with the error: library(BiocManager) Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2…

This study is aimed at revealing the transgenerational effects of thia. We chose the developmental window from embryonic days 6.5 to E15.5 because of its importance in germ cell program establishment. The mice breeding was described in the Materials and Methods section “Mouse treatment and dissection.” The design of the…

Subjects The study was conducted in accordance with the Declaration of Helsinki and all subjects or their parents/guardian gave informed written consent for genetic testing. DNA testing and storage in the Beta Cell Research Bank was approved by the Wales Research Ethics Committee 5 Bangor (REC 17/WA/0327, IRAS project ID…

Downstream analysis with DEseq2 normalization 0 Hi All, I am trying to integrate RNA-seq with Proteomics dataset. I used the DEseq2 for normalization dataset. I have 2 questions for next step: I aim to compute z-score for RNA-seq data. I understand that the normalization from DEseq2 does not take the…

Normalization function in DEseq2 1 Hi all, I am try to work with normalization count data using DEseq2. I am trying their tutorial, until the normalization part. dds <- estimateSizeFactors(dds) There are different output from their code: counts(dds, normalized=TRUE) with when I compute manually: counts(dds, normalized=FALSE) / sizeFactors(dds) The author…

Does DESeq2 correct for library size when importing the counts with DESeqDataSetFromMatrix? 0 Hello, I normally run DESeq2 by importing the data with tximport. However, this time I was given a counts csv file and imported the counts with DESeqDataSetFromMatrix. I noticed that when I create the dds object with…

Diffbind low p-value but high FDR 0 I guess my issue is related to this post support.bioconductor.org/p/85487/#85490. Here is the dba.report(DBA,th=1, bCounts=TRUE) results. One of the peaks clearly shows a significant difference in IGV (And we also expected it to be changed) and has a small p.vaule but the FDR…

Hello Biostars, I have been stuck on an issue for quite some time now, and I hope someone can help me or point me in the right direction. I’ve received my bulk RNA fastq files and analyzed it in R using DESeq2. I have found an article that provide snRNA-seq…

DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment 0 @724e8e11 Last seen 3 hours ago Australia Hi everyone, first time poster. I have resorted to this because I can’t seem to find substantive answers to my question (or don’t exactly fit my question), nor…

Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…

Mice The research conducted in this study complied with all of the relevant ethical regulations. The animal protocols were approved by and performed in accordance with the Institutional Animal Care and Use Committee of St. Jude Children’s Research Hospital. C57BL/6, OT-I50, pmel51 and Rosa26-Cas9 knock-in52 mice were purchased from The…

Dear all, I am doing a DGEA with DESeq2 and data imported with tximport. I have an unbalanced dataset as reported below. With the counts and the metadata that I have I would like to answer different questions. I would like to look at the differential expressed genes between the…

Help understanding DESEq2 and nbinomWaldTest 0 Hi, I just want to understand first, when you put confounders in your DESeq object model, are they regressed out or just accounted for. Second, why is the nbinomwald test used when in DESeq2 is already is getting you log2 fold changes with p…

DOI: 10.18129/B9.bioc.DESeq2   This is the development version of DESeq2; for the stable release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: Development (3.19) Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

DOI: 10.18129/B9.bioc.CAGEr     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CAGEr. Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining Bioconductor version: 3.9 Preprocessing of CAGE sequencing data, identification and…

Same sequencing sample in multiple lanes. How to analyse it? 1 Hi, I have the following samples: Lane 1: 184631_S1_L001_trimmed_R1.fastq 184631_S1_L001_trimmed_R2.fastq Lane 2: 184631_S1_L001_trimmed_R1.fastq 184631_S1_L001_trimmed_R2.fastq I would like to align these fastq files to the reference library. Bowtie2 is the tool I am using. As you can see, the same…

We are doing a comparison between two outcomes (positive and negative). We could not have any positive controls as we do not have any “control” data to set as baseline, either from literature or otherwise. No spike-ins have been used. We have some samples which had no resolved outcome, hence…

filtering lowly expressed exons 0 To reduce false positive testing in differential expression, genes with zero or low counts are pre-filtered. I’m wondering what the equivalent is for this with DEXSeq. the ‘minCount’ argument in estimateDispersions does not work with the latest available release (3.18) on bioconductor. It’s also recommended…

For the Imageable Genome project, we developed a data pipeline that identifies texts containing radiotracers, recognizes and extracts names of radiotracers from texts, filters for clinically relevant radiotracers and their associated targets, and translates protein names, i.e. of radiotracer targets, to names of the coding genes. We then downloaded the…

DESeq2 for microbiome data: raw counts or percentages? 1 @antonkratz-8836 Last seen 9 hours ago Japan, Tokyo, The Systems Biology Insti… Given an OTU table (rows are microbiota and columns are samples) and I want to compare treatment vs placebo sample groups using DESeq2. It is not clear to me…