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• Identify Upregulated Genes From Ranks
  Possible Duplicate: Identify expressed genes from combined microarray data sets Hi all,...
• RPKM, FPKM, TPM, TMM... using the right value for different tasks
  Hi, I would like to be sure I am using the right metrics for 3 different tasks I am performing o...
• Identify Expressed Genes From Combined Microarray Data Sets
  Hi all, I have to combine two datasets obtained using two different platforms (Illumina and Affy...
• Single-cell RNA-seq Outlier Identification : How can I find the subset of genes that are expressed in a common set of samples (cells) ? (Fluidigm SINGuLAR package)
   I have a matrix of single-cell gene expression, containing gene names and cell (sample) IDs. Th...
• using different microarray datasets (meta-analysis?) for DEG pipeline
  First, I apologize if my question seems duplicated, I've extensively searched and read the previo...
• How to distinguish malignant vs non-malignant cells based on gene expression data?
  Hi all, I have a data set of scRNA-seq of a tumor bulk which consists of malignant and non-malig...
• Subgrouping SIngle Cell in RNA-Seq Data Analysis
  Hello dear one, I have a single cell RNA seq data of 100 cells which express -marker A. I want t...
• Gene expression meta-analysis: How to correctly compile a data set.
  Hi all. I am doing my first gene expression meta-analysis, and basically, the way that I thought...
• Best method to do clustering (sub-group) single cell RNA-Seq data?
  Hi Dear one, I have 50 single cell RNA seq data of neuronal cells, I want to find the differen...
• For Mean Expression/FC Calculations in scRNA-seq, should I use All cells or only Expressed Cells?
  I'm doing a differential test for monocle and they show that differentialGeneTest() gives the fea...
• ConsensusClusterPlus error "Memory limit reached"
  Dear community, I want to use ConsensusClusterPlus R package to estimate the number of clusters ...
• pathway for single cell RNA-seq
  I have a single cell RNA-seq data form 10X genomics. I want to perform pathway analysis of top 5...
• How to classify cells based on the expression of genes in scRNA-seq
  Hi, I am analyzing the scRNA-seq data for breast cancer. Here I want to classify the cells into ...
• DEsingle differential-expression analysis
  Hi, I am running DEsingle (https://pubmed.ncbi.nlm.nih.gov/29688277-desingle-for-detecting-three...
• Co-expression analysis of single cell RNA seq data to identify pathway associations
  Hi there. Sorry in advance for the lengthy background - I think it's necessary. My background is...
• Determining Which Genes Are Unexpressed In Cell Lines
  I would like to come up with a list of genes that are not expressed in certain cell lines (e.g. H...
• GSEA with single cell seq data
  I have 130 single cell RNA seq TPMs (all normalized to 1E6 reads).  ~30 can be clearly distinguis...
• Single Cell RNA-seq Mitochondrial Gene Expression
  Hi, I am analyzing a Single Cell RNA-seq data set and most of the top highly variables genes are ...
• Interpreting 2 RNA-seq data with different lengths
  Hi, I am doing a course project which I was asked to analyse RNAseq data. For this analysis I pi...
• Should I remove zero-value from my single cell expression matrix before doing differential test?
  If I have an expression matrix with 2 conditions, A and B, and 30 cells in A condition, 40 cells ...
• How to find significant genes in one-group samples in RNA-seq data?
  Hi everyone, I have log2 transformed TPM data of a single-cell RNA-seq experiment. I have select...
• Query about Z-scores
  Hi everyone! Apologies in advance for the long winded question! Basically, I have been accessing...
• The purpose of scaling to a negative binomial distribution in single cell RNA-seq
  Hi, I'm still a bit new to computational analysis of single cell data, but I'm doing my best to ...