User: EagleEye

gravatar for EagleEye
EagleEye5.0k
Reputation:
5,020
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Trusted
Location:
Sweden
Website:
https://www.researchga...
Twitter:
gridhrahakshi
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Google Scholar Page
Last seen:
3 hours ago
Joined:
3 years, 8 months ago
Email:
s***************@gmail.com

Investigating field of biology by applying logics of computer science, statistics and mathematics.

Posts by EagleEye

<prev • 812 results • page 1 of 82 • next >
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Comment: C: Could not locate a HISAT2 index to basename
... please report the error message ...
written 3 days ago by EagleEye5.0k
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Comment: C: edgeR RPKM Values
... Yes because your code is wrong. Example: rpkm<-rpkm(d,gene.data) ’gene.data’ has extra column of gene names in the first column. It just needs gene length colum. Try this in your above code, it might work. rpkm<-rpkm(d$counts,gene.data[,2]) Else below mentioned complete sample c ...
written 9 days ago by EagleEye5.0k
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Comment: C: edgeR RPKM Values
... group <- c(rep("Sample1",2),rep("Sample1",2)) Why do you have same sample names ('Sample1') for both group. I assume it is, group <- c(rep("Sample1",2),rep("Sample2",2)) Sample Code: data_raw <- read.table("counts.txt", header = T, sep='\t', row.names=1) # Assumed i ...
written 15 days ago by EagleEye5.0k
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Comment: C: GSEA results from RNA-Seq data of different patients are shared! weird!
... When you have doubt verify the results with other tools available for gene enrichment analysis. ...
written 18 days ago by EagleEye5.0k
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Comment: C: DNA Motif discovery from a large number of FASTA sequences
... **2. Background Selection (findMotifs.pl/findMotifsGenome.pl)** If the background sequences were not explicitly defined, HOMER will automatically select them for you. If you are using genomic positions, sequences will be randomly selected from the genome, matched for GC% content (to make GC norma ...
written 21 days ago by EagleEye5.0k
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Answer: A: DNA Motif discovery from a large number of FASTA sequences
... Try Homer, http://homer.ucsd.edu/homer/motif/ ...
written 22 days ago by EagleEye5.0k
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Comment: C: Clinical Survival data of TCGA
... The link I have mentioned above will work. ...
written 4 weeks ago by EagleEye5.0k
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... HI, I have a list of 54000 gene-ids I want to annotate all the genes. Is there any other R package or command-line software that I can use? **Answer:** Make this as separate post/question on Biostars. You will get quick help. ...
written 8 weeks ago by EagleEye5.0k
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hi, In GeneSCF you can only use Gene Symbols ([Example][1]) or Entrez GeneIDs ([Example][2]) as input. And the reason for the error you mentioned is because your input gene list does not match with the database consists of only Gene symbols and Entrez IDs ([Check reported issue][3]). It is also cl ...
written 8 weeks ago by EagleEye5.0k
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hi, COMMAND-: ./prepare_database -db=GO -org=goa_human ERROR-: rm: cannot remove '/home/ibab/software/geneSCF-master-source-v1.1-p2/class/lib/db/gene_info_limit.gz': No such file or directory **Answer:** Do not worry about this error. When it is not found, GeneSCF can download the database. ERROR ...
written 8 weeks ago by EagleEye5.0k

Latest awards to EagleEye

Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 7 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Epic Question 8 months ago, created a question with more than 10,000 views. For Gene Set Clustering based on Functional annotation (GeneSCF)
Scholar 8 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Scholar 8 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to look up GO terms in BioMart using GI ID or Accession ID
Scholar 8 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 9 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Appreciated 10 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 10 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Scholar 11 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?

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