User: EagleEye
EagleEye • 5.3k
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Investigating field of biology by applying logics of computer science, statistics and mathematics.
Posts by EagleEye
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... Here are few journals to consider,
- BMC Bioinformatics
- PLOS Computational Biology
- GigaScience
- Nucleic Acids Research
- Genome Biology (Software)
...
written 3 hours ago by
EagleEye • 5.3k
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... With [GeneSCF][1] batch run, you can try all those database with single run. Selecting the database depends on your experiment or study or interest.
KEGG always gives you broad perspective of pathway terms (metabolism, gene regulation, cellular processes, disease and signaling pathways).
In Gene ...
written 3 days ago by
EagleEye • 5.3k
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... Hi,
My point was, there are evidence for both positive and negative correlation with good publications. So there is no general rule that sense and antisense are globally anti-correlated or positively correlated. There are many factors contributing to that (some times it is species dependent too).
...
written 5 days ago by
EagleEye • 5.3k
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... Hi, I do not think these statements are true "since antisense transcripts usually have opposite expression dynamics than their sense counterparts" and "in a condition, if a gene is overexpressed, there is a good chance that its antisense will be underexpressed". If you are talking about natural anti ...
written 6 days ago by
EagleEye • 5.3k
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... Because your rownames (First row) are same and you asked R to read the file by considering first row as rownames (row.names=1). Because of indexing issue R cannot take same name for multiple rows.
In your case it looks like your fourth column seems to be non-repetitive. You can consider using row.n ...
written 10 days ago by
EagleEye • 5.3k
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... Report the R function you used to read your file. Also provide exact error message. ...
written 10 days ago by
EagleEye • 5.3k
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...
Hi
**KEGG**: http://rest.kegg.jp/list/organism
**Gene Ontology**: http://www.geneontology.org/gene-associations/go_annotation_metadata.all.json
**Reactome & NCG**: Human only
You can also find this information on [GeneSCF documentation][1] under heading '**3. Preparing database**'. Also the ...
written 10 days ago by
EagleEye • 5.3k
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128
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... This post will give you some idea,
https://www.biostars.org/p/207680/#207685
I would recommend you to perform DE analysis separately (since protein coding expression might create biasness due to its abundance). ...
written 11 days ago by
EagleEye • 5.3k
3
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69
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... What happens If you provide this parameter just with SPACE in double quotes for plotProfile,
--regionsLabel " "
...
written 11 days ago by
EagleEye • 5.3k
0
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100
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... From where did you get this name "r.4357_4358ins4358-2785_4358-2719" ? source !!! ...
written 12 days ago by
EagleEye • 5.3k
Latest awards to EagleEye
Teacher
5 days ago,
created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Appreciated
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For A: How to check the type of identifier from ensembl?
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created a comment with at least 3 up-votes.
For C: Survey: What colour theme do you use in your terminal?
Scholar
11 days ago,
created an answer that has been accepted.
For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher
11 days ago,
created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Teacher
17 days ago,
created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Teacher
17 days ago,
created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Scholar
17 days ago,
created an answer that has been accepted.
For A: How to interpret the result of GO analysis using Ontologizer ?
Great Question
20 days ago,
created a question with more than 5,000 views.
For RNA-seq differential expression analysis, which aligner to choose between BWA/tophat/Bowtie?
Teacher
25 days ago,
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For A: How to check the type of identifier from ensembl?
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For New article on TCGA data & useful resource: Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
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For A: Something better than GSEA?
Teacher
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created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Popular Question
12 weeks ago,
created a question with more than 1,000 views.
For New article on TCGA data & useful resource: Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Popular Question
4 months ago,
created a question with more than 1,000 views.
For New article on TCGA data & useful resource: Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: How to check the type of identifier from ensembl?
Appreciated
6 months ago,
created a post with more than 5 votes.
For A: How to check the type of identifier from ensembl?
Good Answer
6 months ago,
created an answer that was upvoted at least 5 times.
For A: Something better than GSEA?
Popular Question
6 months ago,
created a question with more than 1,000 views.
For RNA-seq differential expression analysis, which aligner to choose between BWA/tophat/Bowtie?
Appreciated
7 months ago,
created a post with more than 5 votes.
For A: How to check the type of identifier from ensembl?
Appreciated
9 months ago,
created a post with more than 5 votes.
For A: How to check the type of identifier from ensembl?
Epic Question
10 months ago,
created a question with more than 10,000 views.
For Gene Set Clustering based on Functional annotation (GeneSCF)
Scholar
10 months ago,
created an answer that has been accepted.
For A: How to interpret the result of GO analysis using Ontologizer ?
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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