User: Buffo

gravatar for Buffo
Buffo1.7k
Reputation:
1,730
Status:
Trusted
Location:
Last seen:
4 hours ago
Joined:
3 years, 7 months ago
Email:
c****************@hotmail.com

Posts by Buffo

<prev • 356 results • page 1 of 36 • next >
0
votes
1
answer
76
views
1
answers
Answer: A: converting accession numbers to Gene Symbol
... [BioDBnet][1] is the most easy way :) [1]: https://biodbnet-abcc.ncifcrf.gov/ ...
written 13 days ago by Buffo1.7k
1
vote
1
answer
415
views
1
answers
Comment: C: Which is better: webgestalt vs david?
... 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 Buffo1.7k
2
votes
2
answers
211
views
2
answers
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 Buffo1.7k
0
votes
0
answers
87
views
0
answers
Comment: C: Detect synthetic miRNA via miRDeep2
... It is simply not possible, you need the precursor sequence. ...
written 7 weeks ago by Buffo1.7k
1
vote
0
answers
210
views
0
answers
Comment: C: *.rnk file preparation for GSEA analysis
... 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 Buffo1.7k
0
votes
1
answer
387
views
1
answers
Comment: C: gene sequence fetching from bam or fastq file of rna seq data
... 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 Buffo1.7k
0
votes
1
answer
142
views
1
answers
Comment: C: REACTOME and Ingenuity Pathway Analysis have inconsistent results
... 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 Buffo1.7k
1
vote
1
answer
142
views
1
answers
Answer: A: REACTOME and Ingenuity Pathway Analysis have inconsistent results
... 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 Buffo1.7k
0
votes
2
answers
2.9k
views
2
answers
Comment: C: How to color nodes in Cytoscape according to expression of genes? How should the
... Hi, do you know if it is possible to extract the assigned color code in RGB (or whatever format)? ...
written 10 weeks ago by Buffo1.7k
0
votes
2
answers
164
views
2
answers
Answer: A: how to identify gene expression and genes responsible for virulence
... 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 Buffo1.7k

Latest awards to Buffo

Popular Question 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 ?
Popular Question 5 months ago, created a question with more than 1,000 views. 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 ?
Popular Question 11 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Commentator 11 months ago, created a comment with at least 3 up-votes. For A: GO analysis of Soybean
Popular Question 12 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Commentator 13 months ago, created a comment with at least 3 up-votes. For A: GO analysis of Soybean
Popular Question 13 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 14 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 15 months ago, created a question with more than 1,000 views. 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, created a question with more than 1,000 views. For piRNA target-interaction database?
Popular Question 17 months ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Guru 19 months ago, received more than 100 upvotes.
Scholar 19 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How can I get FASTA if i have Names of proteins ?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How to convert GTF to gff file for read count using HTSeq
Scholar 20 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2057 users visited in the last hour