User: sciencer

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sciencer70
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Posts by sciencer

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How to check how many gene ontology terms sourced from manually curated versus electronic annotations?
... How to check how many gene ontology terms sourced from manually curated versus electronic annotations? I used geneontology.org (pantherdb) for analysis. ...
R rna-seq written 8 months ago by sciencer70 • updated 8 months ago by Jean-Karim Heriche17k
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How to rank differentially expressed genes (output from EBSeq)?
... Hi, How to rank differentially expressed genes? I used EBSeq to find DE genes. Thanks ...
R rna-seq written 8 months ago by sciencer70
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Comment: C: How many samples suggested to perform differential gene expression analysis?
... What else I should do swabarnes2 ? I use EBSeq not DESeq. ...
written 8 months ago by sciencer70
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Comment: C: How many samples suggested to perform differential gene expression analysis?
... Hi nick, I use EBSeq, which have me around 2000 upregulated & 3000 downregulated genes with FDR set to 5%. Is that fine? ...
written 8 months ago by sciencer70
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How many samples suggested to perform differential gene expression analysis?
... Hi, I have 64 single cell RNA sequences when I cluster them (supervised clustering using monocle) I get two clusters 6 samples each. Is it enough to perform differential gene expression analysis? Or how many samples suggested? thanks! ...
R rna-seq written 8 months ago by sciencer70 • updated 8 months ago by Nick20
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Comment: C: How to perform gene ontology analysis with list of upregulated and down regulate
... Sure, Thanks ............! ...
written 8 months ago by sciencer70
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Comment: C: How to perform gene ontology analysis with list of upregulated and down regulate
... thank you, I will check them! ...
written 8 months ago by sciencer70
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Comment: C: How to perform gene ontology analysis with list of upregulated and down regulate
... Hi, Thanks for your reply, yeah.. I fixed FDR= 0.05, then I had 6000 genes totally I segregated them by taking Fold change <1 and Fold change >1 to get up& down regulated genes. Is this okay? p.s. providing FDR is to subset the data which has PPDE greater than or equal to 0.95. ...
written 8 months ago by sciencer70
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How to perform gene ontology analysis with list of upregulated and down regulated genes?
... Hi, I have found ~3000 upregulated genes and ~3000 downregulated genes using RSEM & EBSeq. Using this gene list, how can I perform a Gene ontology analysis in a best way. I would like to produce good diagrams. Please advise best data bases for GO and softwares for diagrams. My data has neural ...
R rna-seq written 8 months ago by sciencer70 • updated 8 months ago by tyaoi210
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Comment: C: How to delete the cells belongs to particlar CellType in R?
... thank you so much! now i understood! ...
written 8 months ago by sciencer70

Latest awards to sciencer

Rising Star 9 months ago, created 50 posts within first three months of joining.
Supporter 10 months ago, voted at least 25 times.

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