User: Sirus
Sirus • 770
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Bioinformatics student
Posts by Sirus
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... 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 17 months ago by
Sirus • 770
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... 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 17 months ago by
Sirus • 770
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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 18 months ago by
Sirus • 770
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... 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 18 months ago by
Sirus • 770
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... @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 21 months ago by
Sirus • 770
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... 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 22 months ago by
Sirus • 770
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... 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 22 months ago by
Sirus • 770
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... 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 23 months ago by
Sirus • 770
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... Are they from the same tumor or they are different ones ? ...
written 2.9 years ago by
Sirus • 770
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... Yeah,
A more elaborated model is in the jmosaics model
http://www.genomebiology.com/2013/14/4/R38
...
written 3.1 years ago by
Sirus • 770
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