User: Sirus

gravatar for Sirus
Sirus770
Reputation:
770
Status:
Trusted
Location:
Boston/USA
Website:
http://www.bioinfo4ara...
Last seen:
10 months ago
Joined:
8 years, 1 month ago
Email:
d*******@gmail.com

Bioinformatics student

Posts by Sirus

<prev • 79 results • page 1 of 8 • next >
0
votes
2
answers
1.6k
views
2
answers
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 14 months ago by Sirus770
1
vote
2
answers
572
views
2
answers
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 14 months ago by Sirus770
0
votes
2
answers
480
views
2
answers
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 14 months ago by Sirus770
0
votes
3
answers
3.5k
views
3
answers
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 15 months ago by Sirus770
2
votes
1
answer
509
views
1
answers
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 18 months ago by Sirus770
1
vote
1
answer
509
views
1
answers
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 18 months ago by Sirus770
2
votes
7
answers
4.8k
views
7
answers
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 19 months ago by Sirus770
0
votes
3
answers
1.4k
views
3
answers
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 20 months ago by Sirus770
0
votes
0
answers
977
views
0
answers
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 2.7 years ago by Sirus770
0
votes
1
answer
3.0k
views
1
answers
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 2.8 years ago by Sirus770

Latest awards to Sirus

Great Question 12 months ago, created a question with more than 5,000 views. For What Are The Obsolete Research Topics In Bioinformatics?
Scholar 18 months ago, created an answer that has been accepted. For A: Could you suggest me a proper feature selection method for mixed type variable d
Popular Question 2.2 years ago, created a question with more than 1,000 views. For What Are The Obsolete Research Topics In Bioinformatics?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Mapping Of Uniprot Ids To Mips Ids
Popular Question 2.3 years ago, created a question with more than 1,000 views. For What Is The Best Way To Calculate The Distance Between Two Proteins?
Voter 2.4 years ago, voted more than 100 times.
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Mapping Of Uniprot Ids To Mips Ids
Appreciated 2.6 years ago, created a post with more than 5 votes. For What Are The Obsolete Research Topics In Bioinformatics?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For How To Get The Go Associated With A Protein?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For What Are The Obsolete Research Topics In Bioinformatics?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Calculate The Weighted Mean Of Matrix In R: Fastest Way
Popular Question 3.5 years ago, created a question with more than 1,000 views. For What Are The Obsolete Research Topics In Bioinformatics?
Great Question 3.9 years ago, created a question with more than 5,000 views. For What Are The Obsolete Research Topics In Bioinformatics?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For What Are The Obsolete Research Topics In Bioinformatics?
Student 4.3 years ago, asked a question with at least 3 up-votes. For What Are The Obsolete Research Topics In Bioinformatics?
Appreciated 4.3 years ago, created a post with more than 5 votes. For What Are The Obsolete Research Topics In Bioinformatics?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For What Are The Obsolete Research Topics In Bioinformatics?
Supporter 4.6 years ago, voted at least 25 times.
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Converting Affymetrix (*_At) Mouse Probe Id To Hugo Gene Symbol In R
Librarian 7.2 years ago, created a post with more than 10 bookmarks. For What Are The Obsolete Research Topics In Bioinformatics?
Prophet 7.2 years ago, created a post with more than 20 followers. For What Are The Obsolete Research Topics In Bioinformatics?
Popular Question 7.2 years ago, created a question with more than 1,000 views. For What Are The Obsolete Research Topics In Bioinformatics?
Good Question 7.2 years ago, asked a question that was upvoted at least 5 times. For What Are The Obsolete Research Topics In Bioinformatics?
Student 7.2 years ago, asked a question with at least 3 up-votes. For What Are The Obsolete Research Topics In Bioinformatics?
Appreciated 7.2 years ago, created a post with more than 5 votes. For What Are The Obsolete Research Topics In Bioinformatics?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 969 users visited in the last hour