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• Differential gene expression using R studio
  Hello everyone, I am new to r-studio and I have to do differential gene expression analysis for ...
• Gene expression analysis on gene counts from different genome builds
  Hello all, I will do a differential gene expression analysis using Deseq2. However in my count d...
• RNA-seq analysis: How to output normalized counts or normalized FPKM values for all genes in each condition from DESeq2 pipeline?
  I am using a “star-featurecounts-DESeq2” pipeline to perform transcriptome comparison between sev...
• Dealing With Read Counts Under Pe And Se Scenarios
  Hi, I am unsure how to deal with this case to go about analysing RNA-seq data. Suppose that you...
• differential expression of human sample showing 63000 genes in output
  Hello all Recently i got human rna seq sample for differential expression analysis I used htseq-c...
• Filtering RNA-seq expression matrix?
  Hello, I am currently in the process of analyzing RNA-sequencing data and would love to have you...
• Differential Expression of Splice Junctions using voom-limma/voom-diffSplice
  Hello guys, I am interested in the differential expression of splice junctions. For this purpos...
• Differential analysis using cell-line data with replicate information
  I have a total of 8 samples, 4 controls and 4 Foxcut gene over expressed samples. The column dat...
• Filtering in RNA-Seq to get Differentially Expressed lncRNA
  Hi All, I am quite new to RNA-Seq analysis and I have some confusion as to how to perform certai...
• differential gene expression analysis
  I'm trying to do differential gene expression analysis (RNA-Seq data) using Limma and EdgeR How c...
• Post Deseq2 Analysis
  Hi All, I have Differential gene expression (DGE) results between TCGA-LUSC & TCGA-LUAD samp...
• Requesting help with RNA-Seq differential gene analysis
  Hello, I am performing RNA-Seq data analysis to find differentially expressed genes in my data. ...
• RNA-seq analysis: How to generate a master gene expression matrix to do co-expression cross all conditions of my samples
  I am trying to perform gene co-expression analysis to identify the clusters of genes that co-expr...
• DE Analysis starting from TPM matrix? Also, no replicates.
  I have a matrix of TPM values from 27 different tissue types that I obtained from a database (thu...
• Differential Expression of a normalized RNAseq expression dataset
  I have a RNAseq expression matrix obtained from TCGA (TCGA-GBM) it's been normalized. The columns...
• Deseq2 results have too many genes
  Hello everyone, I am trying to validate a RNA-Seq analysis pipeline but whatever I do (like same ...
• differential expression based on multiple biological repeats
  Hi, I downloaded the raw data from the current GTEX release (http://www.gtexportal.org/home/). I...
• Comparing gene expression between two samples
  Hi, I have raw read count matrix of HTG EdgeSeq for two patients **A** and **B**; I have tumour ...
• How to evaluate the similarity between two different samples by using RNA-Seq?
  Hi, there! I have two samples' RNA-Seq data, one is amniotic epithelial cells(AEC), and another ...
• Co-expression network using Cytoscape
  Hi I have mrNA expression and LncRNA expression data from RNASeq. I have calculated the correlat...
• differential expression analysis tools for single end reads
  Hi, Which tool would be preferable to detect differentially expressed genes between human contro...
• DE analysis with two samples in multiple samples
  I use `EdgeR` to perform DE analysis using the standard protocol. The steps are as follows. 1....
• Differential Expression Analysis When Most Features Are Not Expected To Be Unchanged?
  I have an RNA-seq dataset that is looking at small RNAs. I am using blockbuster to group my mappe...