Moderator: h.mon

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h.mon30k
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Posts by h.mon

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Comment: C: Adding gene set to GSVA
... How come you ask about using `getGmt()`, and then you use `getBroadSets()`? Why don't you try `getGmt()`? And no, don't call the new object **c2BroadSets**, it will overwrite the existing **c2BroadSets** from GSVAdata, if the package has been loaded. ...
written 3 hours ago by h.mon30k
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Answer: A: Adding gene set to GSVA
... The problem is you will have to create the **C6: oncogenic signatures** yourself, because they are not included in any package. The tutorial you linked to works because **c2BroadSets** is included in the package GSVAdata. The GSVAdata has this description on how **c2BroadSets** was created: >The ...
written 4 hours ago by h.mon30k
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Comment: C: Create table of gene expression for multiple samples
... See if the answer here is of any help: https://www.biostars.org/p/350099/#350133 ...
written 6 hours ago by h.mon30k
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Comment: C: Reads mapped with zero quality still mapped to exactly one position
... Look at the SAM flags (the second field from a SAM record), it could shed some light on this issue: samtools view algn_srt.bam "chr21:43063074-43063074" | cut -f 2 | sort | uniq -c ...
written 7 hours ago by h.mon30k
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Answer: A: Fasta Taxonomy Annotation
... >For my situation, are there any ways or scripts to produce my own taxonomy database in fasta format? Although you can use any taxonomic classification pipeline to "annotate" your own fasta file (I would use DADA2+phyloseq for this, but a huge combination of tools could do the work), your annota ...
written 7 hours ago by h.mon30k
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Answer: A: What does metaFlye mean by "corrected reads"?
... Raw Nanopore reads have a high error rate - I believe it is currently at 10-15%, but someone more knowledgeable may correct me. Corrected reads are reads with a "low" error rate, of less than 3%. I think the correction method doesn't matter, as long as the error rate is lower than 3%. ...
written 18 hours ago by h.mon30k
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Comment: C: GFF3 to GTF problems
... When installing bioinformatics tools with conda, do not install them at the base environment, create an environment for the tool - environments will prevent this sort of conflict between incompatible program versions. conda create -n genometools genometools conda activate genometools The f ...
written 18 hours ago by h.mon30k
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Comment: C: Unequal group size
... This is a purely statistics question, you should ask it at a more appropriate venue, such as [Cross Validated][1]. P.S.: I also did a search for you, here are some results: [Wilcoxon Rank Sum test unequal sample sizes][2] [t test with drastically different sample sizes][3] [1]: https://stats ...
written 18 hours ago by h.mon30k
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Answer: C: DE analysis with limma (What to include in the model?)
... limma was developed for microarray data. One can use limma for for RNAseq analysis, using the voom transformation, are you using it? I am almost certain I have seen the same question discussed in depth before, either here at BioStars or at the BioConductor support forum. However, I can't find any r ...
written 18 hours ago by h.mon30k
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Answer: A: EdgeR and contrasts: How to compare with a group not in the model
... Check [edgeR Users Guide][1], chapter 3.3, on how to define the contrasts for such a complex design. For me, the approach that works better (as in, it is easier to understand) is the one described in section 3.3.1. Start by creating a composite `group` variable: group <- factor( paste0( pati ...
written 23 hours ago by h.mon30k

Latest awards to h.mon

Appreciated 7 hours ago, created a post with more than 5 votes. For C: Kraken2 vs Minimap2 and Blast results seem to be incongruent
Teacher 17 hours ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Appreciated 5 weeks ago, created a post with more than 5 votes. For Where did EMBOSS go?
Scholar 6 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Scholar 8 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Appreciated 8 weeks ago, created a post with more than 5 votes. For C: Kraken2 vs Minimap2 and Blast results seem to be incongruent
Scholar 10 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Appreciated 11 weeks ago, created a post with more than 5 votes. For Where did EMBOSS go?
Scholar 3 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Scholar 3 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 4 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 4 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Appreciated 4 months ago, created a post with more than 5 votes. For C: Kraken2 vs Minimap2 and Blast results seem to be incongruent
Appreciated 4 months ago, created a post with more than 5 votes. For C: Kraken2 vs Minimap2 and Blast results seem to be incongruent
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate

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