User: pixie@bioinfo

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pixie@bioinfo1.2k
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PhD Student

Posts by pixie@bioinfo

<prev • 146 results • page 1 of 15 • next >
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Answer: A: RNA Seq data for WGCNA
... You could go for a normal mutual-rank based correlation network or a pearson correlation network using a high threshold cutoff for the correlation values. You can then use any clustering algorithm/plugin in cytoscape to cluster your networks. Biological validations using functional/pathway enrichme ...
written 5 days ago by pixie@bioinfo1.2k
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Answer: A: Gene ontology and KEGG pathway analysis of rice RNA-seq data
... You can use MapMan. I found that it has more gene annotations for rice than other tools. It has to be locally installed together with the specific annotation file for the species. More details here: https://mapman.gabipd.org/ ...
written 26 days ago by pixie@bioinfo1.2k
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Answer: A: Pathway analysis programs
... All genes may not be enzyme coding, and may not be annotated for biochemical pathways. GO enrichment might be another option to consider. ...
written 5 weeks ago by pixie@bioinfo1.2k
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Comment: C: WGCNA and VisAnt
... What was the edge weight cutoff you chose to export ? ...
written 5 weeks ago by pixie@bioinfo1.2k
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Regarding p-value for calculating enrichment in MapMan software
... Hello, Is there anyone using the MapMan pathway /ontology analysis software ? I am having trouble to understand how are the p-values calculated using the Wilcoxon Rank Sum Test. I uploaded a list of genes (both DEGs and non-DEGs). It calculated p-values for the bins. For one such bin, i noticed tha ...
mapman written 5 weeks ago by pixie@bioinfo1.2k
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Comment: C: How to plot Z-scores in R for gene expression data
... Thank you so much,I finally could do it. You saved a lot of time for me ! ...
written 10 weeks ago by pixie@bioinfo1.2k
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Comment: C: How to plot Z-scores in R for gene expression data
... Actually, MultiExperiment Viewer (MeV) creates clusters and then we can visualize plots. Here, I have already clustered my data and wish to visualize ...
written 10 weeks ago by pixie@bioinfo1.2k
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Comment: C: How to plot Z-scores in R for gene expression data
... Thanks, am looking into it. ...
written 10 weeks ago by pixie@bioinfo1.2k
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How to plot Z-scores in R for gene expression data
... Hello, I have a table with gene expressions across samples. I have calculated the z scores and need to create this plot as given below: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022196#pone-0022196-g001 My table looks like: `Gene_name E_2401_ctrl_1 E_2401_ctrl_2 E_2401_ctr ...
gene expression written 10 weeks ago by pixie@bioinfo1.2k • updated 10 weeks ago by rice.researcher80
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Comment: C: Regarding getting gene count tables for DeSeq from StringTie using prepDE.py
... Thank you for the reply. What I had meant was, most of my gene IDs are missing in the gene count tables and are replaced with the StringTie IDs (MSTRG). When I looked into the merged gtf file, I saw that the gene ids (of the transcripts) are not present in the count table, rather the MSTRG IDs are ...
written 11 weeks ago by pixie@bioinfo1.2k

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Scholar 5 days ago, created an answer that has been accepted. For A: RNA Seq data for WGCNA
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Internship opportunities for PhD students ?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Removing rRNA and tRNA sequences using GTF files
Popular Question 10 weeks ago, created a question with more than 1,000 views. For T Cell Specific Gene Expression Data
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Great Question 8 months ago, created a question with more than 5,000 views. For How Do I Get The Gene Names From The Chromosome Locations In A Wig File
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Popular Question 14 months ago, created a question with more than 1,000 views. For Database In Python For Storing Microarray Files
Great Question 14 months ago, created a question with more than 5,000 views. For How Do I Get The Gene Names From The Chromosome Locations In A Wig File
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