User: unawaz

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unawaz40
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Location:
Australia
Website:
https://github.com/una...
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urwahnawaz
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1 year, 1 month ago
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Posts by unawaz

<prev • 19 results • page 1 of 2 • next >
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Hi Kevin, Thanks again for the amazing tool! Can I use EnhancedVolcano with plotly? I assume it's built using ggplot2, and I've tried to do: `ggplotly(plot)` where plot is a volcano plot made using EnhancedVolcano. I get the following error message though: ```Error in unique.default(x) : `` ...
written 4 days ago by unawaz40
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... That's unfortunate. Thanks for looking though! ...
written 7 weeks ago by unawaz40
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... This is the output for sleuth, where b is equivalent to Log2FC ``ens_gene ext_gene target_id pval qval b se_b mean_obs var_obs tech_var sigma_sq smooth_sigma_sq final_sigma_sq `` ...
written 7 weeks ago by unawaz40
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Hi Kevin, Great tool! I've been pretty much using it for all my volcano plots. I wanted to know if there was a way to use EnhancedVolcanos with results from sleuth? cheers! ...
written 8 weeks ago by unawaz40
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Comment: C: Differential expression: replicates in one condition, no replicates in the other
... Coming back to this, I came across this package OUTRIDER which is able to find DEGs compared to controls in an n=1 situation. I haven't tried it myself, but might be worth looking at it: Paper: https://www.sciencedirect.com/science/article/pii/S0002929718304014 ...
written 8 weeks ago by unawaz40
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Is it appropriate to apply RUVseq on output from kallisto?
... Hi, I've ran kallisto on my samples, and summarized the transcript level counts to gene level counts to perform a differential gene expression analysis. I'm also interested in differential transcript expression, which I will perform using Sleuth. Exploratory analysis at the gene level revealed t ...
batchcorrection kallisto rna-seq written 8 weeks ago by unawaz40 • updated 8 weeks ago by kristoffer.vittingseerup1.6k
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Comment: C: to get each covariate with PC loading in PCA
... Do you have a file phenotype data? This file should include the name of your samples, conditions and any other information such as batch etc. You can use that and perform a PCA analysis in R. Make sure your counts are normalised! ...
written 9 weeks ago by unawaz40
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What's your preferred pathway enrichment analysis tool after DEG analysis and why?
... So firstly, I'm completely aware that this type of question has been asked multiple times (I know this since I've been scrolling over these type of questions for the past 2 days), but I'm actually more interested in knowing the reasons as to why some people prefer I've performed differential expre ...
gene ontology rna-seq written 9 weeks ago by unawaz40 • updated 9 weeks ago by Jean-Karim Heriche18k
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Answer: A: Differential expression: replicates in one condition, no replicates in the other
... I've actually had a similar issue to yours and the way I resolved it was: downloading more controls from public databases. We were using LCLs, so we them from geuvadis. I also did an outlier detection analysis in which I calculated Z-scores and looked for the genes in my patient that did not look l ...
written 9 weeks ago by unawaz40
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Answer: A: RNA-Seq data analysis mapping to closest genome as reference genome
... It depends on how closely related the two organisms are. Otherwise you can perform a de novo transcriptome assembly using tools like Trinity (https://github.com/trinityrnaseq/trinityrnaseq/wiki), and then BLAST it against the genome of the closely related one. ...
written 10 weeks ago by unawaz40

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Supporter 12 weeks ago, voted at least 25 times.

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