User: Sakti

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Sakti390
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1 year, 7 months ago
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Posts by Sakti

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Comment: C: Clustering of CNV genomic coordinates, take 2
... Thanks a lot Sean! I was pondering the genomic bins solution, which seems what will work in the end for my data. Thanks!! ...
written 19 months ago by Sakti390
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Comment: C: Clustering of CNV genomic coordinates, take 2
... Hi Sean, thanks for commenting. I have updated the post with the answers to your questions. ...
written 19 months ago by Sakti390
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Clustering of CNV genomic coordinates, take 2
... Dear Biostars, After searching the internet for quite a while, I have yet to find an easy solution for clustering of human genomic coordinates. This [post][1] asked the same question a couple of years ago, but there was no answer as to how one could simply cluster a bed file and be able to graph it ...
genomic coordinates cluster analysis cnv bed written 19 months ago by Sakti390 • updated 19 months ago by Sean Davis25k
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Comment: C: Matplotlib comprehensive chromosome drawing
... Beautiful reply, and great code to continue with my Python and matlib trainings. I really appreciate your reply, and hope it's useful for more Biostarters!!! ...
written 4.2 years ago by Sakti390
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Comment: C: how to retrieve mouse (mm10) gene information from Ensemble using Biomart inR
... The current Ensembl database should be mm10, the most up to date one. For changing genomic versions see my reply. ...
written 4.2 years ago by Sakti390
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Answer: A: how to retrieve mouse (mm10) gene information from Ensemble using Biomart inR
... library(biomaRt) ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl") annot<-getBM(c("ensembl_gene_id", "mgi_symbol", "chromosome_name", "strand", "start_position", "end_position","gene_biotype"), mart=ensembl) #For older biomart releases I have used ensembl <- useMart("ENSEM ...
written 4.2 years ago by Sakti390
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Matplotlib comprehensive chromosome drawing
... Hello Biostars, Ryan Dale posted 4 years ago a wonderful answer to the question of how to start your own chromosome plots using Python's Matplotlib https://www.biostars.org/p/9922/. I am migrating from Perl to Python and have been bashing my head for 3 days trying to add extra lines and gene annot ...
gene python chromosome matplotlib plot written 4.2 years ago by Sakti390 • updated 3.5 years ago by fransua390
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Comment: C: How to calculate chromosomal enrichment of differentially expressed genes
... Wonderful post, very informative. Thanks for sharing the function with us! ...
written 4.2 years ago by Sakti390
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Scatter plotting DE values along a contiguous chromosomal x axis
... Dear Biostars, I am trying to make a scatterplot to show my RNA-Seq log2fold values along all the chromosomal positions for the human genome. Something like this:                 |  ***                    ***                  **        *   *** log2fold |  *    **   ***      *              ***   ...
R de rna-seq graph written 4.6 years ago by Sakti390
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Answer: A: bedtools:intersectBed - how to get overpapping information?
... intersectBed will always give you the intersect segments from your datafile overlapping the other features. But seems that what you want to do is simply attach the annotation.bed overlap info onto your original main.bed file. If you're familiar with perl you can write a small script where you save a ...
written 4.6 years ago by Sakti390

Latest awards to Sakti

Great Question 4.0 years ago, created a question with more than 5,000 views. For Argtable2.H Installation On Ubuntu
Prophet 4.0 years ago, created a post with more than 20 followers. For What Does Samtools Flagstat Results Mean?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How to calculate chromosomal enrichment of differentially expressed genes
Great Question 4.0 years ago, created a question with more than 5,000 views. For What Does Samtools Flagstat Results Mean?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Coordinate Correspondences Between Mouse Reference Genome And Sanger Mouse Genomes
Popular Question 4.0 years ago, created a question with more than 1,000 views. For What Does Samtools Flagstat Results Mean?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Problems Using Formatdb And Fastacmd
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Bioinfo Exe That Can'T Be Executed, Due To Missing /Lib64/Ld-Linux-X86-64.So.2
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: how to retrieve mouse (mm10) gene information from Ensemble using Biomart inR
Popular Question 4.2 years ago, created a question with more than 1,000 views. For What Does Samtools Flagstat Results Mean?
Appreciated 4.2 years ago, created a post with more than 5 votes. For Bioconductor For Large Bam File Analysis
Good Question 4.2 years ago, asked a question that was upvoted at least 5 times. For Bioconductor For Large Bam File Analysis
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Bioconductor For Large Bam File Analysis
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Argtable2.H Installation On Ubuntu
Student 5.0 years ago, asked a question with at least 3 up-votes. For What Does Samtools Flagstat Results Mean?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Samtools Header From A Bacterial Genome Ba File
Epic Question 5.5 years ago, created a question with more than 10,000 views. For What Does Samtools Flagstat Results Mean?
Good Question 5.5 years ago, asked a question that was upvoted at least 5 times. For Bioconductor For Large Bam File Analysis
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Argtable2.H Installation On Ubuntu
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Argtable2.H Installation On Ubuntu
Great Question 8.0 years ago, created a question with more than 5,000 views. For What Does Samtools Flagstat Results Mean?
Popular Question 8.0 years ago, created a question with more than 1,000 views. For What Does Samtools Flagstat Results Mean?
Student 8.2 years ago, asked a question with at least 3 up-votes. For Bioconductor For Large Bam File Analysis
Appreciated 8.2 years ago, created a post with more than 5 votes. For Bioconductor For Large Bam File Analysis
Popular Question 8.2 years ago, created a question with more than 1,000 views. For Bioconductor For Large Bam File Analysis

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