User: Buffo
Buffo • 1.7k
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Posts by Buffo
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... [BioDBnet][1] is the most easy way :)
[1]: https://biodbnet-abcc.ncifcrf.gov/ ...
written 13 days ago by
Buffo • 1.7k
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... I am not sure if is faster but agree with "nice plots", however, it does not use a ranked list as WebGestalt. In my opinion it is a very important advantage for most uses. ...
written 19 days ago by
Buffo • 1.7k
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Answer:
A: Question about miRNAs
... No, 5p and 3p are different miRNAs, they come from the same precursor and are partially complementary in sequence but they may have completely different targets. Personally I recommend you not mix data from different databases, miRBase, mirpath from DianaTools and mirdeep2 works fine for me in hsa d ...
written 6 weeks ago by
Buffo • 1.7k
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... It is simply not possible, you need the precursor sequence. ...
written 7 weeks ago by
Buffo • 1.7k
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... Filter by FDR looks good for me, however filtering by an arbitrary FC may be a source of bias. I usually filter by FDR, and use the complete matrix (log2fold as rank). Ranked list for Webgestalt is a two column list, gene and rank (logfold). ...
written 7 weeks ago by
Buffo • 1.7k
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... load your bam files in [IGV][1] and check if that gene has SNPs among samples. That sequence is the same because the genome reference is exactly the same.
[1]: https://software.broadinstitute.org/software/igv/ ...
written 8 weeks ago by
Buffo • 1.7k
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... If you have expression data I suggest you to use [webgestalt][1], it uses a ranked list. It is very easy to use and very accurate, at least for human and mouse.
[1]: http://www.webgestalt.org/ ...
written 9 weeks ago by
Buffo • 1.7k
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... It is supposed that IPA is a deeply curated and larger database than other public ones. If it is true, obtain different results would be normal, but you can compare the number of related genes on each pathway and how do they deal with redundancy. ...
written 9 weeks ago by
Buffo • 1.7k
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... Hi, do you know if it is possible to extract the assigned color code in RGB (or whatever format)? ...
written 10 weeks ago by
Buffo • 1.7k
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... Q1. Yes, you can identify bacteria by 16S amplification and sequencing.
Q2. Yes, you can perform differential expression analysis before treatment/after treatment (do not forget replicates, at least 3). Genome reference is recommended but if it does not exist you can perform a de novo transcriptome ...
written 10 weeks ago by
Buffo • 1.7k
Latest awards to Buffo
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4 months ago,
created a question with more than 1,000 views.
For HISAT2 indexes, GRCm38 or mm10?
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
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5 months ago,
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For piRNA target-interaction database?
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
Appreciated
8 months ago,
created a post with more than 5 votes.
For A: Which is better: webgestalt vs david?
Scholar
8 months ago,
created an answer that has been accepted.
For A: How can I get FASTA if i have Names of proteins ?
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
Appreciated
8 months ago,
created a post with more than 5 votes.
For A: Which is better: webgestalt vs david?
Scholar
8 months ago,
created an answer that has been accepted.
For A: How can I get FASTA if i have Names of proteins ?
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
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11 months ago,
created a question with more than 1,000 views.
For Pipeline for genome annotation?
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11 months ago,
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For A: GO analysis of Soybean
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12 months ago,
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For Pipeline for genome annotation?
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13 months ago,
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For A: GO analysis of Soybean
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13 months ago,
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For Pipeline for genome annotation?
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14 months ago,
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For Pipeline for genome annotation?
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15 months ago,
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For Pipeline for genome annotation?
Popular Question
15 months ago,
created a question with more than 1,000 views.
For piRNA target-interaction database?
Popular Question
15 months ago,
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For piRNA target-interaction database?
Popular Question
17 months ago,
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For piRNA target-interaction database?
Guru
19 months ago,
received more than 100 upvotes.
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19 months ago,
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For A: How can I get FASTA if i have Names of proteins ?
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For A: How can I get FASTA if i have Names of proteins ?
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For A: How to convert GTF to gff file for read count using HTSeq
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20 months ago,
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For A: How can I get FASTA if i have Names of proteins ?
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