User: Sirus

gravatar for Sirus
Sirus770
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770
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Boston/USA
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http://www.bioinfo4ara...
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4 hours ago
Joined:
7 years, 1 month ago
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Bioinformatics student

Posts by Sirus

<prev • 79 results • page 1 of 8 • next >
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Answer: A: What is the best way to measure similarities / correlations of gene expression t
... I think you can get inspired by single-cell methods to detect differentially expressed gene along the pseudo-time. Different techniques have been developed to detect cyclic genes ([here][1]) and genes that show a significantly differential expression along the pseudo-time (such as [here][2] and [her ...
written 10 weeks ago by Sirus770
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Answer: A: What is the point of standardizing each gene in gene expression data?
... I think it is just for visualization purposes. Suppose that you use a certain threshold to select a group of genes to display (expl: RPM>1), the highly expressed genes will skew the scale in your heatmap, which will make some genes (that are also highly expressed in the same group of samples) se ...
written 12 weeks ago by Sirus770
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Answer: A: Qc of Bisulfite Fastq file
... At the fastq level, you cannot tell much I think, just the quality of the sequencing. However, you can check some other metrics after mapping, such as the conversion rate (especially if you have a spike-in lambda genome). You can also check the mapped and un-mapped reads, the CpG and non-CpG site ...
written 12 weeks ago by Sirus770
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Answer: A: bash script for RNA seq alignment with STAR
... You can to use [**bpipe**][1], to automate and parallelize your pipeline. For example, you can create a file `STAR_mapping.groovy` then write your script as follow (supposing that you already have done the adaptor trimming and quality control) runSTAR = { def prefix="/alignment/treg_NB ...
written 3 months ago by Sirus770
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Answer: A: Could you suggest me a proper feature selection method for mixed type variable d
... @morovatunc , to avoid over-fitting, you can use all your data but by doing for example 10-fold cross-validation (the Caret package can do that for you). Then you'll get your variable importance. Because theoretically, the signal that you'll find important is supposed to be important in any subse ...
written 6 months ago by Sirus770
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Comment: C: Could you suggest me a proper feature selection method for mixed type variable d
... There are many ways in which you can do it. Random forest are a good choice, after training you can look at the "variable importance" which will rank the variables of your model according to their contribution to the prediction. You can check the section of [variable importance][1] section of the C ...
written 6 months ago by Sirus770
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Comment: C: StackExchange/Area51 bioinformatics is back
... It is much more different, bioconductor support is mainly to help with the questions related to bioconductor packages and R programming in bioinformatics, while Biostars is a general bioinformatics plateform. A new SE site similar to biostars will not bring any thing new. ...
written 7 months ago by Sirus770
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Answer: A: intersect multiple bed files in R
... You can use the `findOverlapsOfPeaks` function from the [ChIPpeakAnno][1] package. Just to make the code more easy to follow, I use the `readBroadPeak` function from the genomation package. But you don't need to use too many packages to do that. Suppose you have 3 bed files in the boradPeak forma ...
written 8 months ago by Sirus770
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Comment: C: without normal control, can I know a gene's expression level only by its express
... Are they from the same tumor or they are different ones ? ...
written 20 months ago by Sirus770
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Comment: C: Chip-Seq, Get Highly Enriched Regions For A Certain Mark Within One Sample
... Yeah,  A more elaborated model is in the jmosaics model  http://www.genomebiology.com/2013/14/4/R38 ...
written 22 months ago by Sirus770

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