User: biofalconch

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biofalconch460
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Mexico
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an hour ago
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5 years, 11 months ago
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Posts by biofalconch

<prev • 94 results • page 1 of 10 • next >
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Answer: A: How to visualise KEGG pathway?
... I think the r package [Pathway][1] is the one you are looking for :) [1]: http://pathview.r-forge.r-project.org/#:~:text=The%20pathview%20R%20package%20is,and%20specify%20the%20target%20pathway.&text=Currently%20only%20KEGG%20pathways%20are%20implemented. ...
written 8 days ago by biofalconch460
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Comment: C: DESeq DataSet from HTSeqCount Error
... My guess is that in the table you are loading the genes as an extra column, thats why the number of columns are not matching ...
written 9 days ago by biofalconch460
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Answer: C: Convert .sam to .bam without producing writing .sam file to storage space
... I think he means if there is a way of piping it to generate a bam file directly without going through a sam file intermidiate. Something like this would be my guess: bowtie2 -x Index -1 Reads1.fq -2 Reads2.fq | samtools view -b -h -o output.bam ...
written 9 days ago by biofalconch460
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Comment: C: How do determine the ratio of mRNA:rRNA:ncRNA in an RNA-seq dataset?
... Take a look in rfam.xfam.org ;) ...
written 4 months ago by biofalconch460
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Comment: C: Differential gene expression, starting from RSEM expected count values.
... tximport was developed by the same guys that developed edgeR. The concern that lead to the creation of the package as I understand it is that people make omission of the assumptions these packages work on (in this case, that counts are raw counts and not extimates), so they decided to create a packa ...
written 4 months ago by biofalconch460
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Comment: C: miRDeep2 stops at 'excising precursors' step..
... Have you considered running each part separately? It might help you pinpoint which step is causing trouble. ...
written 4 months ago by biofalconch460
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Answer: A: How are GO biological processes and pathways related?
... There are two different consortiums all together friend. the Gene Ontology identifiers start with GO, while KEGG start with KO. GO terms tend to be more specific most of the times, depending how deep in the hierarchy you go into, while KO terms tend to be more broad. Their organization is different ...
written 4 months ago by biofalconch460
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Comment: C: How to convert a text file into gtf file?\
... A little bit more info would be appreciated, but maybe you can do it re-ordering the columns. See more abour the GTF format [Here][1] [1]: https://www.ensembl.org/info/website/upload/gff.html ...
written 5 months ago by biofalconch460
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Answer: A: Use PWM from CISBP-rna to find motif with MEME (FIMO)
... Maybe a little bit late but here is a workaround I did. You have to transpose the matrix so that it looks like this: GeneID A: 0.5 0.5 0 C: 0 0 0.5 G: 0.5 0 0 T: 0 0.5 0.5 I'm not going to post the script since it is a little convoluted but the only thing is ...
written 8 months ago by biofalconch460
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Answer: C: topGo analysis with PANTHER.db
... Have a look at section 4.3 of the manual, it might help ...
written 8 months ago by biofalconch460

Latest awards to biofalconch

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: PBS script on cluster
Popular Question 21 months ago, created a question with more than 1,000 views. For RNA-seq Differential Expression Analysis
Popular Question 23 months ago, created a question with more than 1,000 views. For RNA-seq Differential Expression Analysis
Popular Question 23 months ago, created a question with more than 1,000 views. For small non-coding RNA
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: PBS script on cluster
Popular Question 24 months ago, created a question with more than 1,000 views. For RNA-seq Differential Expression Analysis
Popular Question 2.1 years ago, created a question with more than 1,000 views. For RNA-seq Differential Expression Analysis
Popular Question 2.2 years ago, created a question with more than 1,000 views. For RNA-seq Differential Expression Analysis
Popular Question 2.5 years ago, created a question with more than 1,000 views. For miRNA aligment with miRBase parameters
Voter 2.6 years ago, voted more than 100 times.
Popular Question 2.7 years ago, created a question with more than 1,000 views. For miRNA aligment with miRBase parameters
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: plant housekeeping genes without paralogs
Supporter 3.7 years ago, voted at least 25 times.

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