User: lihe.liu

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lihe.liu20
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Posts by lihe.liu

<prev • 16 results • page 1 of 2 • next >
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What is a good way to get all Gene Ontology terms for a certain species in R?
... Hi community, I wonder what is a good way/package to get all the GO terms for a certain species in R. I work with Bos taurus, and I tried **Ensembl** and **org.Bt.eg.db** database, however, they give me quite a different number of GOs. Seems that Ensembl has way more GOs than org.Bt.eg.db. org ...
R gene ontology written 7 months ago by lihe.liu20 • updated 7 months ago by Biostar ♦♦ 20
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Answer: A: gene ontology with reference list
... Another way could be: - Download all the GO information (ID, Name, and genes involved) from a certain database (e.g. **Ensembl** or **org.xx.eg.db**) - Extract every GO category and the genes involved. - Run a loop, for each GO, compose a 2 by 2 contingency table and get corresponding p-value using ...
written 7 months ago by lihe.liu20
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Comment: C: How to deal with the missing values after converting genes to Entrez Gene ID usi
... Hi Emily, Quick question, in terms of GO records (Bos taurus), are **Ensembl** database and **org.Bt.eg.db** database very different? I was trying to get **all** the GO involved in my species, but these two give me quite different numbers of GO. Is this normal? What is a good way to get all the ...
written 7 months ago by lihe.liu20
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Comment: C: How to deal with the missing values after converting genes to Entrez Gene ID usi
... That makes sense to me! Thank you so much! ...
written 8 months ago by lihe.liu20
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Comment: C: How to deal with the missing values after converting genes to Entrez Gene ID usi
... Thank you so much!!! ...
written 8 months ago by lihe.liu20
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How to deal with the missing values after converting genes to Entrez Gene ID using BioMart?
... Hi, I was trying to convert a list of genes to EntrezID, in my list, I have either **enternal_gene_name** or **entrezgene_accession**, and I need to convert them to EntrezID level. I tried BioMart: library(biomaRt) ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="btaurus_gene_ensem ...
R biomart written 8 months ago by lihe.liu20 • updated 8 months ago by Emily_Ensembl20k
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Comment: C: Conda install package - different internals
... I never used it neither (And I don't think it is necessary on Mac, perhaps?). We were doing troubleshooting and we just noticed this is a difference and potentially could be an issue...... ...
written 9 months ago by lihe.liu20
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Comment: C: Conda install package - different internals
... May I ask what is gonna print out if you do "echo $R_HOME". Do we have to specify R_HOME in **.bash_profile** on our Macs? My friend who is using Conda has the R path (same as which R in that env) printed out if he do "echo $R_HOME". Is this potentially a problem? Thank you! ...
written 9 months ago by lihe.liu20
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Comment: C: Conda install package - different internals
... Installation somehow broke as shown. type = 'source' added but it won't proceed. https://ibb.co/wynZSRn Something wrong? ...
written 9 months ago by lihe.liu20
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Comment: C: Conda install package - different internals
... I will try to find that. And also I think conda install works well. For now I am struggling with some errors: For package "**clusterProfiler**": 1. Error: package or namespace load failed for ‘DOSE’: package ‘GOSemSim’ was installed by an R version with different internals; it needs to be re ...
written 9 months ago by lihe.liu20 • updated 9 months ago by RamRS27k

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Popular Question 6 months ago, created a question with more than 1,000 views. For Conda install package - different internals

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