User: unawaz

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unawaz40
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Location:
Australia
Website:
https://github.com/una...
Twitter:
urwahnawaz
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15 hours ago
Joined:
11 months ago
Email:
a*******@student.adelaide.edu.au

Posts by unawaz

<prev • 15 results • page 1 of 2 • next >
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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 1 day 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 3 days ago by unawaz40 • updated 1 day ago by kristoffer.vittingseerup1.2k
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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 8 days 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 8 days ago by unawaz40 • updated 8 days ago by Jean-Karim Heriche17k
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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 8 days 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 16 days ago by unawaz40
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Comment: C: Appropriate to apply RUVSeq to exon bin counts for DEXSeq?
... I'm having similar issues. Did you ever find an answer for your question? ...
written 19 days ago by unawaz40
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Comment: C: Is there a way to get the name or IDs of genes with the goseq table?
... Exactly what I needed! Thank you! ...
written 29 days ago by unawaz40
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Is there a way to get the name or IDs of genes with the goseq table?
... Hi all, I've performed a GO enrichment analysis using goseq. The output of ``goseq()`` tells you the enriched categories with how many significant genes are in the categories etc, but it doesn't give you the ID of genes that are in any of those categories. Obviously you can use ``getgo()`` to re ...
gene ontology goseq rna-seq written 4 weeks ago by unawaz40 • updated 4 weeks ago by magicpants60
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How to make a gene expression correlation graph?
... Hi all, I have two gene lists that I created using edgeR of two different conditions. I want to see the direction of commonly expressed genes and make a graph [like this][2] for person's correlation. Would I use R for this sort of analysis, and use person's correlation to compare the logFC for bot ...
R rna-seq edger written 11 weeks ago by unawaz40 • updated 11 weeks ago by h.mon22k

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