User: unawaz

gravatar for unawaz
unawaz40
Reputation:
40
Status:
New User
Location:
Australia
Website:
https://github.com/una...
Twitter:
urwahnawaz
Last seen:
10 hours ago
Joined:
1 year, 5 months ago
Email:
a*******@student.adelaide.edu.au

Posts by unawaz

<prev • 21 results • page 1 of 3 • next >
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Comment: C: ClusterProfiler : What is GeneRatio and BgRatio?
... I'm a little confused about these terms. When I;ve used the same gene set, why do my numbers of n and N change when doing gene ontology for different categories. For example, for the same gene list for an overrepresentation test in Biological Processes for taxis GeneRatio is 209/3770 and BGRatio ...
written 6 weeks ago by unawaz40
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Comment: C: Concatenating fastq.gz files across lanes
... Hi, This has been a really useful script! Just wanted to know if there is a way to change it so that I can run when my fastq files are in different sub-directories? Currently it only works if they are in the same one. Cheers! ...
written 12 weeks ago by unawaz40
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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 months 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 5 months 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 5 months 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 5 months 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 6 months 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 6 months ago by unawaz40 • updated 6 months ago by kristoffer.vittingseerup2.0k
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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 6 months 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 6 months ago by unawaz40 • updated 6 months ago by Jean-Karim Heriche20k

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Supporter 7 months ago, voted at least 25 times.

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