User: steve

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steve2.7k
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Posts by steve

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Comment: C: Software for clinical interpretation of variants
... ANNOVAR works fine and has great features. Most of my issues end up coming from the licensing required for ANNOVAR for commercial use (you start building some small pipeline then suddenly your company/institute wants to deploy it as part of a product), and also the input & output formats. I end ...
written 4 weeks ago by steve2.7k
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Answer: A: Software for clinical interpretation of variants
... As far as databases, I have also used PMKB ( https://pmkb.weill.cornell.edu/ ) in the past, and there is also OncoKB ( https://www.oncokb.org/ ). I was going to mention N-of-One but it seems like [Qiagen has already acquired them](https://corporate.qiagen.com/newsroom/press-releases/2019/20190107_qi ...
written 4 weeks ago by steve2.7k
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Comment: C: Is there any solution to reduce the size of .RData?
... Is this an `.Rdata` file that you are generating yourself? Or is this the file that you let R maintain with your interactive R sessions? Because if its the latter then the best solution is to just stop letting R save your interactive sessions. ...
written 5 weeks ago by steve2.7k
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Comment: C: BioFlows - Container-enabled Bioinformatics pipeline engine
... not sure I would fault a program for something it wasnt designed to do ...
written 6 weeks ago by steve2.7k
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Comment: C: BioFlows - Container-enabled Bioinformatics pipeline engine
... congrats on the release. Since there are [many workflow frameworks](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems) out there, it might be helpful to include a comparison of Bioflows to other systems, especially CWL, Nextflow, and Snakemake, since ...
written 6 weeks ago by steve2.7k
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Answer: A: Is there a reasonable way to rank peaks that are common between replicates?
... Maybe I am missing something, but isnt this what DiffBind does? https://www.bioconductor.org/packages/devel/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf Been using it for years to detect differentially bound peaks across groups and replicates for ChIP-Seq. ...
written 6 weeks ago by steve2.7k
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Comment: C: How to count the number of alignments in a bam file without using samtools?
... dont think I have ever seen a case where people actually use uncompressed bam file, at that point you might as well be using sam format ...
written 7 weeks ago by steve2.7k
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How to count the number of alignments in a bam file without using samtools?
... Preferably, using either standard GNU tools, or perhaps something in the Python standard library. Any ideas? ...
bam written 7 weeks ago by steve2.7k • updated 7 weeks ago by xiaoguang50
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Answer: A: Merging lots of csv files in on master one
... You can do it easily in Python #!/usr/bin/env python3 """ $ cat file1.csv k1,c1 k2,c1 k3,c1 $ cat file2.csv k1,c2 k2,c2 k3,c2 $ cat file3.csv k1,c3 k2,c3 k3,c3 $ ./script.py file1.csv file2.csv file3.csv k1,c1,c2,c3 ...
written 7 weeks ago by steve2.7k
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Comment: C: bioinformatics career choice - could use guidance
... There are a number of Bioinformatics courses available on Coursera that include programming; https://www.coursera.org/search?query=bioinformatics& You might try going through some of these, and building up a GitHub profile with programming examples of tools or workflows you have made (de novo, ...
written 10 weeks ago by steve2.7k

Latest awards to steve

Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Laptop Suggestion to handle Bioinformatics Softwares?
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Appreciated 6 weeks ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Appreciated 6 weeks ago, created a post with more than 5 votes. For How to run CWL with Nextflow
Great Question 7 weeks ago, created a question with more than 5,000 views. For Creating chromosome karyotype plot with R and ggplot2
Epic Question 12 weeks ago, created a question with more than 10,000 views. For Creating chromosome karyotype plot with R and ggplot2
Great Question 6 months ago, created a question with more than 5,000 views. For Creating chromosome karyotype plot with R and ggplot2
Appreciated 7 months ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Appreciated 9 months ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Popular Question 10 months ago, created a question with more than 1,000 views. For Are intron mapped reads expected from RNA based reads?
Appreciated 10 months ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Popular Question 11 months ago, created a question with more than 1,000 views. For Are intron mapped reads expected from RNA based reads?
Popular Question 12 months ago, created a question with more than 1,000 views. For Are intron mapped reads expected from RNA based reads?
Popular Question 13 months ago, created a question with more than 1,000 views. For HOMER motif discovery gives inconsistent results on repeated runs
Good Question 14 months ago, asked a question that was upvoted at least 5 times. For How to tell which transcript is the canonical transcript?
Popular Question 15 months ago, created a question with more than 1,000 views. For HOMER motif discovery gives inconsistent results on repeated runs
Scholar 15 months ago, created an answer that has been accepted. For A: HOMER mergePeaks totals don't add up to peaks input
Popular Question 15 months ago, created a question with more than 1,000 views. For HOMER motif discovery gives inconsistent results on repeated runs
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Scholar 17 months ago, created an answer that has been accepted. For A: HOMER mergePeaks totals don't add up to peaks input
Appreciated 17 months ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Student 18 months ago, asked a question with at least 3 up-votes. For How to tell which transcript is the canonical transcript?
Great Question 20 months ago, created a question with more than 5,000 views. For How to tell which transcript is the canonical transcript?

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