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• why no replicate samples in ccle mRNA data
  I notice that in ccle(cancer cell line encyclypedia), the mRNA expression data seldom contains re...
• Finding differentially expressed genes in Control vs. Treated
  I have 2 .cell files containing gene expression data for Control and Treated cell lines (download...
• Problem in selecting threshold value for FPKM
  Hey Folks, I am analyzing the RNA-seq data of cell line. I am comparing two treatment conditions...
• find out whether cell lines are verified
  I have a list of about 1000 cancer cell lines with associated RNA-seq expression profiles per gen...
• replicates in edgeR and DESeq2
  Hi everybody, This my first post here, so first I would like to thank active people on this foru...
• TPM on SingleCell RNASeq
  Hi there to all. I want to analyze an extensive (FACS) single-cell RNASeq dataset, from Tabula Mu...
• Confusion Related To The Experiment R-Th Meta Analysis For Identifying Differential Gene Expression
  I was reading this paper where they say they run r-th meta analysis method to find significant g...
• RNA seq Case Study dataset for differential expression analysis tool validation
  I have developed a tool for differential expression analysis of RNA seq data and now I am looking...
• What "questions" could be answered with the RNAseq data that I have? I need to make my data fit for a certain experiment format.
  I am high-schooler who did a bioinformatics internship over the summer. Since I am pretty young, ...
• How to compare the gene expression signature of treated cancer cell and normal cell
  I have the gene expression signatures of cancer cell lines and cancer cell lines treated with cer...
• identify high and low express genes from cufflinks output
  Hi I want to find high and low express genes from cufflinks output ( genes.fpkm_tacking file) in...
• Remove batch effect for many RNA-seq
  Hello every, I a new comer for RNA-seq, here I have some questions for RNA-seq analysis. I want...
• parameters to DESeq2 for RNA-seq data
  Hi all (: I'm a beginner in bioinformatics and could use some help in RNA-seq analysis i'm worki...
• What are the advantages of using cell-lines over tissue samples of RNA-seq data ?
  Hi, I am working on the cancer samples, it includes the both cell-line samples as well as tissue...
• How To Reduce The Number Of Genes For A Microrray Experiment Done On Cell Lines (Dimensionality Reduction)?
  I have a dataset with 18 cell lines (HG_U133_plus2) normalized using GCRMA. I have collapsed the ...
• Can I perform differential gene expression analysis using the Connectivity Map expression data?
  Dear members of Biostar, I am a Master's student doing a project in differential gene expression...
• Comparing RNAseq Samples
  Hello, I have 2 bacterial strains of the same species I want to perform differential expression ...
• Gene expression comparison of Cancer and Normal tissue
  I have a basic question about RNAseq normalisation while comparing cancer/tumor tissue expression...
• Skipping Clustering in Seurat
  Hello, I was wondering if there is a possibility to skip the clustering step in Seurat and just ...
• How to get the differentially expressed genes in cancer cell lines
  I'm wondering is there a way to calculate the differentially expressed genes in cancer cell lines...