User: guillaume.rbt

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guillaume.rbt770
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Posts by guillaume.rbt

<prev • 212 results • page 1 of 22 • next >
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Comment: C: single cell RNA seq gene co-expression
... Many thanks for the advice. If I want to assess the correlation between two genes without filtering for gene expression I will get many cells with no detected expression for the two genes. Which test would be appropriate to evaluate the expression correlation, while handling for those "missing valu ...
written 6 weeks ago by guillaume.rbt770
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single cell RNA seq gene co-expression
... Hi all, I'm trying to assess the gene expression correlation between a specific gene and all other genes, thanks to a public scRNA seq dataset of human melanoma biopsies.([https://singlecell.broadinstitute.org/single_cell/study/SCP109/melanoma-immunotherapy-resistance#study-summary][1]) For this I ...
scrnaseq gene co-expression written 6 weeks ago by guillaume.rbt770
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Answer: A: Remove variants in VCF with the same call in all but the reference
... You can achieve that with SnpSift filter : http://snpeff.sourceforge.net/SnpSift.html For example if you want to filter out all positions where all your 5 samples are variants : cat variants.vcf | java -jar SnpSift.jar filter "!(isVariant( GEN[0] ) & isVariant( GEN[1] ) & isVariant( GE ...
written 9 weeks ago by guillaume.rbt770
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Comment: C: Any recommendation for pathway analysis of Wheat RNA-seq data?
... What do you mean by "none of my DEGs mapped" ? Have you been able to run agriGO and found no enriched GO? ...
written 10 weeks ago by guillaume.rbt770
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Answer: A: Any recommendation for pathway analysis of Wheat RNA-seq data?
... You can try Agrigo to perform GO enrichment analysis : http://systemsbiology.cau.edu.cn/agriGOv2/ ...
written 10 weeks ago by guillaume.rbt770
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Comment: C: KEGG pathway enrichment analysis for wheat and barley
... I don't know how to do a KEGG pathway enrichment. But I know you could do GO enrichment analysis on with agrigo (http://systemsbiology.cau.edu.cn/agriGOv2/index.php) ...
written 3 months ago by guillaume.rbt770
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Comment: C: RNAseq differential expression analysis : relevance of Immunoglobulin genes enri
... Ok great, I will definitely test it ! ...
written 3 months ago by guillaume.rbt770
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Comment: C: RNAseq differential expression analysis : relevance of Immunoglobulin genes enri
... Ok thank for the tip ! (both markers are indeed also up-regulated :) ) ...
written 3 months ago by guillaume.rbt770
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Comment: C: RNAseq differential expression analysis : relevance of Immunoglobulin genes enri
... Hi Eric and thank for your advices. I have in this case a high number of samples (111). I encountered similar results with what you described in your poster (better results with Limma/voom than with DEseq2 or EdgeR) ...
written 3 months ago by guillaume.rbt770
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Comment: C: RNAseq differential expression analysis : relevance of Immunoglobulin genes enri
... Thank for your questions. The samples are collected before treatment, so the treatment has no effect on the profiles. I try to detect biomarkers that are predictive of a good response. The treatment tested is anti-PD1 checkpoint inhibitors, and it is expected to have a higher immune response activi ...
written 3 months ago by guillaume.rbt770

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