Tag: DEG

DESeq2 input from GDAC firehose

Hi guys, I hope you are fine. I’m not good in English so if you couldn’t understand my question, please feel free to reply. I’m a beginner of bioinformatics. I want to practice differential expressed gene (DEG) analysis in R. The RNA seq data I used was downloaded from broad…

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Identification of differentially expressed genes in AF

Defeng Pan,1,* Yufei Zhou,2,* Shengjue Xiao,1,* Yue Hu,3,* Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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AccuClear Ultra High Sensitivity dsDNA Quantitation Kit with DNA Standard, trial size (200 assays) 31028-T

Description: trial size (200 assays), AccuClear Ultra High Sensitivity dsDNA Quantitation Kit with DNA Standard Category: Nucleic acid quantitation Shipping temperature: 15&deg, C, C to 30&deg Shipping conditions: n/a Storage: 2&deg, C, C to 8&deg Gene target: AccuClear Sensitivity dsDNA Quantitation Kit with DNA trial size (200 assays) Short name:…

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Monocle3 differential expression failed when active.assay is not “RNA”

after run estimate_size_factors, data with active.assay = ‘integrated’ works too, but no deg in the result. > [email protected] = ‘integrated’ > cds_raw <- as.cell_data_set(seurat_object) Warning: Monocle 3 trajectories require cluster partitions, which Seurat does not calculate. Please run ‘cluster_cells’ on your cell_data_set object > cds <- cluster_cells(cds_raw) > pr_graph_test_res <-…

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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter

Enter the body of text here Hi, I am analysing a RNA Seq dataset coming from 3 independent cell isolates (isolate1, isolate2, isolate3), each given 3 different treatments (control, drug1, drug2). We are testing drug 1 against control in the first instance: We also observed that there is some variation…

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How to generate a Venn diagram from edgeR DEG results?

How to generate a Venn diagram from edgeR DEG results? 0 Dear All, I have done DEG analysis of genes from 4 samples using edgeR. I want to plot them (number of DEGs) using a Venn diagram. I have results from pairwise comparisons as UP and DOWN gene list with…

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Problem for analysing GSEA and ORA

Problem for analysing GSEA and ORA 0 I analysed two different GEO dataset individually and found DEG for each dataset .After that I compare the two dataset DEG and found some common DEG.Now i want to analyse GSEA and ORA for that common DEG.As far i know for analysing GSEA…

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Identification of Hub Genes in Patients with Alzheimer Disease and Obs

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

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Re-analysis of multiple scRNAseq data as a combined new one

Re-analysis of multiple scRNAseq data as a combined new one 0 Hi all, There are so many regions in brain.The cortex itself is of many types.I found many single cell RNA seq studies which focus on different regions eg- gse … somatosensory cortex dropseq year 2015 gse….. primary visual cortex…

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Sep 15 | GEO Data Mining and Submission – In Person

Event listing from University of Pittsburgh: Wednesday, September 15 from 10:00 AM to 4:00 PM This workshop will focus on Gene Expression Omnibus (GEO) repository. We will learn how to find high throughput gene expression studies – bulk RNA-seq/ scRNA-seq /microarray from GEO, retrieve gene expression count data and generate…

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Sep 15 | GEO Data Mining and Submission – Online

Event listing from University of Pittsburgh: Wednesday, September 15 from 10:00 AM to 4:00 PM This workshop will focus on Gene Expression Omnibus (GEO) repository. We will learn how to find high throughput gene expression studies – bulk RNA-seq/ scRNA-seq /microarray from GEO, retrieve gene expression count data and generate…

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Gene with hundreds of counts very similar, is it possible to use it to get DEGs?

Gene with hundreds of counts very similar, is it possible to use it to get DEGs? 0 Hi, I’m starting in boinfomatics and I’m using Deseq2 for differential expression analysis. I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from…

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GitHub – HaoWuLab-Bioinformatics/wu-group: ECSWalk

GitHub – HaoWuLab-Bioinformatics/wu-group: ECSWalk Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time ECSWalk: A carcinogenic driver module detection method based on a network model. Data used in this study: In our research, we used data processed by Rafsan Ahmed, et al. and Mark…

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create protein database for local Blast

create protein database for local Blast 1 Hello friends, how’re you? I wanted to know how I can do a blast against a database that I downloaded. I’ve downloaded a database of protein sequences from DEG (essential genes) and my idea is to do a blast against this database in…

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List of human protein coding genes with given name (known function?)

List of human protein coding genes with given name (known function?) 2 Hello, To put it simply, I am doing differential expression analysis on human RNA-seq data and I want to focus my analysis of genes that are: 1) Protein coding, so no SNOR or MIR 2) Genes with a…

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How to transform the deg gene list from seurat to a gene list input to clusterProfiler compareCluster ?

Sorry for lateness, I wanted to do something similar. This is what I did for reference: Using a Seurat generated gene list for input into ClusterProfiler to see the GO or KEGG terms per cluster. I’ll keep the meat and potatoes of the Seurat vignette in this tutorial: library(dplyr) library(Seurat)…

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DEGs with uninsteresed sample files

DEGs with uninsteresed sample files 1 Hi all, I am working on some bulkRNAseq data from GEO and my sample description looks like this. I am interested in A vs B, A vs C and B vs C but I am not interested in sample D. My question is whether…

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How filter genes to construct co-expression network?

How filter genes to construct co-expression network? 1 Hi, I am interested to filter data for constructing co-expression network , Which parameter can i use to filter genes? As i know in WGCNA tutorial, it suggests not to use differential expressed genes(DEG) to filter genes. WGCNA Co-expreesion network DEG Filtering…

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FindMarkers for ClusterProfiler

FindMarkers for ClusterProfiler 1 Hi, I recently ran FindMarkers to compare DEG between two different clusters in a single-cell RNA-seq analysis This is my code: markers= FindMarkers(obj, ident.1=c(4), ident.2 = c(5)) head(markers) dim(markers) table(markers$avg_log2FC > 0) table(markers4v5$p_val_adj < 0.05 & markers$avg_log2FC > 0) I would like to run ClusterProfiler to…

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Power calculation for microarray data

Power calculation for microarray data 0 I have an initial sample of 228 patients from a microarray study. Recently I have obtained a new set of labels specifying different condition types for only 69 out of the 228 patients. I wanted to run a DEG analysis on this set of…

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microarray miRNA expression data analysis

I wrote a script on how to analyze the microarray-based miRNA expression data. Here is my code: # general config baseDir <- ‘.’ annotfile <- ‘mirbase_genelist.tsv’ setwd(baseDir) options(scipen = 99) require(limma) # read in the data targets <- read.csv(“/media/mdrcubuntu/46B85615B8560439/microarray_text_files/targets.txt”, sep=””) # retain information about background via gIsWellAboveBG project <- read.maimages(targets,source=”agilent.median”,green.only…

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