User: cfos4698

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cfos4698130
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Posts by cfos4698

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Example of gene2cat goseq
... I'm currently using GOseq at the moment, and am having some success using helper scripts with Trinity software. As the Trinity developers note, the scripts are intended as a basic guide and customization for your own data set might be necessary. Anyway, the bundled runGOseq.pl script generates anot ...
written 5 months ago by cfos4698130
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Comment: C: Differential expression of all genes vs only annotated genes
... This seems sensible, thanks for suggesting. ...
written 5 months ago by cfos4698130
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Answer: A: Batch correction and DE analysis of miRNA Seq data
... How have you determined the batch effect? A PCA/MDS plot? Batch effects are normally removed from the data set (e.g., using removeBatchEffects) for visualisation purposes. For example, you can observe PCA plots with a) the batch still there; and b) the batch removed. However, you should not feed ba ...
written 5 months ago by cfos4698130
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Answer: A: batch effects of RNAseq data from public databases - need to correct or not ?
... To be confident that any potential batch effect isn't affecting your work, you could always obtain the reads/raw count data and run a differential expression analysis yourself. You could model for any potential batch effect by including the batch in the differential expression model, e.g. ```design ...
written 5 months ago by cfos4698130
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Determining expressed genes when average gene LogCPM distribution is unimodal
... Hi all, Determining which genes are expressed in an RNA-seq experiment is often a little arbitrary, but one method I've seen is to look at the average logCPM distribution of all genes in the data set (described here https://darwinawardwinner.github.io/resume/examples/Salomon/CD4/reports/RNA-seq/sal ...
rnaseq rna-seq written 6 months ago by cfos4698130
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Answer: A: miRNA differential expression
... For point 1: As ATpoint said, one method is not better than the other - each has its own merits. As tough as it is when first starting out, you need to read through the assumptions of the methods and make a judgement call as to which is most appropriate for your data. It's helpful to read through th ...
written 6 months ago by cfos4698130
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Comment: C: Generating consensus sequence from bam file
... I agree with nsmi8446. This is a nice concise way to solve your problem. ...
written 6 months ago by cfos4698130
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Answer: A: Software for Tree Visualization
... There are a variety of packages within R that can be used to plot phylogenetic trees, such as ggtree (as pointed out by tangming2005). These are useful if you want to script the plotting of your trees. However, the packages can be pretty tricky to work with/optimize to get nice-looking, legible tree ...
written 2.3 years ago by cfos4698130
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Answer: A: The best Maximum Parsimony software
... I generally advise against parsimony, but I guess if it could be a useful form of comparison. Two software choices come to mind immediately: PAUP* (http://paup.sc.fsu.edu/downl.html) and TNT (http://www.zmuc.dk/public/phylogeny/tnt/). PAUP* used to require a license, but I'm not sure if this is stil ...
written 2.3 years ago by cfos4698130

Latest awards to cfos4698

Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Software for Tree Visualization
Scholar 2.3 years ago, created an answer that has been accepted. For A: The best Maximum Parsimony software
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Software for Tree Visualization
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Software for Tree Visualization
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Software for Tree Visualization

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