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• Isoforms with opposite read counts and reverse complement sequences
  Hi, I am new to RNAseq and not a bioinformatician so please take my apologies if these are basic ...
• How to answer if the biological process is up or down-regulated?
  When doing enrichment analysis using public pathways databases (e.g. KEGG, Reactome) or ontologie...
• correct order for pathway analysis
  I am doing pathway analysis but there a lot of tutorials so, I am looking for the correct way of ...
• How to select the best isoform for a differential expressed gene in Trinity?
  Hi, I have followed Trinity guidelines and assembled a denovo assembly as well as used that asse...
• How do I obtain logFC values from sleuth results (both genes and isoforms)?
  I have run sleuth (0.28.0) for the first time, and I have results both for isoforms and for genes...
• How to determine Up and Down regulated genes from log2(fold change)of the Cuffdiff output?
  Dear All I ran cuff-links/cuff-diff pipeline on my RNA-seq data. But I have some problem...
• excel and most up/down regulated
  hello everyone, my question is I have a mutant and wild gene analysis in excel. I did t-test and ...
• Showing up and down regulated GO and pathway using enrichR and ggplot2
  Hi guys, I have made this code for showing best 20 up and down GO or Kegg pathway in R using ...
• Up and Down regulated genes
  Hello experts can share your knowledge While analyzing the deferentially expressed genes some pap...
• Gene ontology comparsion between up- and down-regulated genes
  Hi all friends, I did differential expression analysis of an RNA-seq project. Then, using agrigo...
• How to identify down-regulated genes in monocle
  Hi, all Here I used “differentialGeneTest” in monocle to identify differentially expressed genes...
• normalized FPKM matrix file EdgeR and GO Mapping
  Can someone provide me with a clear cut answer to the below: Can I use the normalised .FPKM matr...
• Understanding up and down regulated genes from LOG2 foldchange or foldchange
  Hi friends Today i was confused with a very simple problem !! How to determine up and down regul...
• Problem in analyzing Rice RNA-Seq data
  Hi friends  I have project on Rice RNA-Seq, in this project i have only 1 replicate for each of 3...
• Is There Any Biological Hypothesis Underlying Up- Or Down Regulated Gene Set Enrichment?
  I have just read a paper from cancer research in which they do pathway enrichment using up-regula...
• How to report differentially expressed transcription factors in scatter plot
  **Dear Biostars Friends, Hi** I want to report transcription factors (TFs) that are expressed di...
• Same KEGG pathways enriched by up- and down-regulated genes
  Hi all, I'm working on a project to find out the key characteristics of different cell subclones...
• AUGUSTUS principal isoform
  Hi, I have used AUGUSTUS for gene prediction. It produces multiple isoforms for some genes. The...
• Is fold change of value 1.5 (log2FC = 0.58) a significant value ?
  In Biostars forum for differential gene expression analysis by LIMMA I found that most people sug...
• Why there is the same GO term in the both up- and down-regulated gene set?
  Hi all, I'm busy with doing expression analysis of an RNA-seq project from a non-model organism ...
• Gibbs sampling/bootstrap replicates in Salmon
  This is a sort-of-kind-of follow up to [this post][1]. Say I've performed *de novo* transcriptom...