User: francesca.defilippis

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40
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New User
Location:
European Union
Last seen:
2 years, 8 months ago
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3 years ago
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f*******************@unina.it

Posts by francesca.defilippis

<prev • 18 results • page 2 of 2 • next >
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gage pathways enrichment analysis
... Hello! I'd like to do a pathway enrichment analysis on metagenomic data. I already have the KO IDs for my genes. Does gage support bacteria genomes? than, I saw that you need to specify the organism name, but I'm not interested in a specific bacterial species. Is it possible to use it with KO ids fr ...
pathways gage kegg written 3.0 years ago by francesca.defilippis40 • updated 3.0 years ago by Luo Weijun1.4k
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Comment: C: Pathway enrichment in bacteria metagenomes
... Hi! Thanks for your reply! I didn't understand one thing: how to deal with KO  belonging to different pathways? I mean, of course each KO can belong to different pathways and metabolisms. How do I need to treat them? For example, if I want to do a heatplot at different kegg hierarchy levels , how do ...
written 3.0 years ago by francesca.defilippis40
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Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
... Hi! I have a list of gene IDs from ncbi (starting with >gi....). They are from metagenome analysis, so belong to different bacteria genomes. I'd like to get the corresponding kegg orthology ID (KO....) and kegg pathways (ko....). Can the keggrest package do it? I found only examples specifying th ...
keggorthology keggrest kegg written 3.0 years ago by francesca.defilippis40 • updated 3.0 years ago by James W. MacDonald45k
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GeneAnswer for bacteria metagenomes
... Hi! I'm interested in pathways enrichment analysis of microbial metagenome from human gut. I already have a list if differentially expressed genes, with relatorive KO and eggNog IDs. now I'd like to know if there is an up or down regulation of some specific pathway. I found the geneAnswer package co ...
geneanswers kegg metagenome written 3.0 years ago by francesca.defilippis40 • updated 16 months ago by Guangchuang Yu800
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Pathway enrichment in bacteria metagenomes
... Hello! i'm analysing gut metagenome samples.  I used DeSeq2 to obtain a list of differentially expressed genes. I'd like to explore if an enrichment in specific pathways is present. I have both KO and eggNog IDs of the genes. Is there a tool to get the pathway they belonging to and explore for up ...
metagenomics pathways written 3.0 years ago by francesca.defilippis40 • updated 3.0 years ago by Luo Weijun1.4k
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Comment: C: DESeq2 output explanation
... Hi Michal I have a further question. I read I can use the rlog transformation and use those values for heatplots or pca. Do I need to use raw counts as input for rlog or do I need to normalize for library size before (diving the reads for each gene by the total reads of the sample) thanks! ...
written 3.0 years ago by francesca.defilippis40
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Comment: C: DESeq2 output explanation
... Hi Michael, thanks for your reply. I read both the vignette and the tutorial, but I still didn't find the information I'm looking for.  If I extract the results for a specific contrast, let see A vs B, how can I know if the log2 fold changes are referred to A or B?   ...
written 3.0 years ago by francesca.defilippis40
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DESeq2 output explanation
... Hello! I have a question about the results of differential expression analysis in deseq2. I did: DEgenes=results(DEcd, contrast=c("clD", "V", "VG")) and I got the table with the log2 fold change and the p values. But what I didn't understand is to which group the fold change refer to. So if I ha ...
deseq deseq2 written 3.0 years ago by francesca.defilippis40 • updated 3.0 years ago by Michael Love15k

Latest awards to francesca.defilippis

Popular Question 2.7 years ago, created a question with more than 1,000 views. For DESeq2 output explanation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For DESeq2 rlog transformation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For DESeq2 rlog transformation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Pathway enrichment in bacteria metagenomes
Popular Question 2.7 years ago, created a question with more than 1,000 views. For gage pathways enrichment analysis
Great Question 2.7 years ago, created a question with more than 5,000 views. For DESeq2 output explanation

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