User: steve

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Posts by steve

<prev • 188 results • page 1 of 19 • next >
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Comment: C: Merging individual .bed files?
... for what kind of purposes were you planning to use this merged file? ...
written 11 days ago by steve1.5k
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Answer: A: Create a File format to store Variant
... Another format I recently learned about is from the HL7 FHIR standard: https://www.hl7.org/fhir/genomics.html https://www.hl7.org/fhir/sequence-example-fda.json.html ...
written 26 days ago by steve1.5k
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Comment: C: generation of heat map by excel data.
... a third comment; it looks like the Excel sheet you are trying to import has 2-line headers. Your best bet is to clean this up in Excel prior to importing, to make the headers 1-line only. Or you can try to wrangle it in R ...
written 27 days ago by steve1.5k
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Comment: C: generation of heat map by excel data.
... Also you can look at `ggplot2` for this, cheatsheet [here](https://www.rstudio.com/wp-content/uploads/2015/03/ggplot2-cheatsheet.pdf), particularly look at `geom_tile` function. However you will need to use something like `reshape2` to convert your dataframe to 'long' format, description [here](http ...
written 27 days ago by steve1.5k
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Comment: C: generation of heat map by excel data.
... if your data is already in R, then it is most helpful to provide the `dput()` output of a small selection of the data (`head()`), something like this: `dput(head(df))` then copy/paste this output. This allows others to recreate the exact R object you are working with. ...
written 27 days ago by steve1.5k
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Comment: C: FastQC with multiple FASTQ files
... +1 for MultiQC, I dont even bother to look at the individual output metrics anymore ...
written 27 days ago by steve1.5k
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Comment: C: FastQC with multiple FASTQ files
... or [Nextflow](https://www.nextflow.io/). Examples of using FastQC inside a Nextflow pipeline [here](https://github.com/nextflow-io/hack17-tutorial/blob/master/script7.nf), [here](https://github.com/NYU-Molecular-Pathology/demux-nf/blob/4adf55bdfcc237e998be711bb17f29c80906f84f/main.nf#L180) and [here ...
written 27 days ago by steve1.5k
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Comment: C: Creating Interactive Volcano Plots with R and Plot.ly
... Not sure I understand the question, since the original post documents all the R code used in this example. The transcript regulation values were produced using [DiffBind](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) using the ChIP-Seq workflow from [this pipeline](https://githu ...
written 4 weeks ago by steve1.5k
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IBM Power8/Power9 servers for bioinformatics?
... Does anyone have experience using these machines that they could share? One of the draws for them is the large number of CPU logical cores available on a single chip, upwards of 100-200+ using SMT4 or SMT8, which means a single server could handle as many parallel threads as are typically spread acr ...
server ibm genomics written 5 weeks ago by steve1.5k
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Comment: C: What Is Your Favorite Question To Ask When Interviewing Potential Bioinformatici
... I find these a lot more relevant than many other questions posted here. ...
written 6 weeks ago by steve1.5k

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Popular Question 3 months ago, created a question with more than 1,000 views. For HOMER mergePeaks totals don't add up to peaks input
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Epic Question 4 months ago, created a question with more than 10,000 views. For Creating Interactive Volcano Plots with R and Plot.ly
Librarian 4 months ago, created a post with more than 10 bookmarks. For Creating Interactive Volcano Plots with R and Plot.ly
Popular Question 4 months ago, created a question with more than 1,000 views. For HOMER mergePeaks totals don't add up to peaks input
Popular Question 4 months ago, created a question with more than 1,000 views. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Scholar 5 months ago, created an answer that has been accepted. For A: HOMER mergePeaks totals don't add up to peaks input
Popular Question 6 months ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?
Popular Question 7 months ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
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Appreciated 8 months ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
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Great Question 10 months ago, created a question with more than 5,000 views. For Creating Interactive Volcano Plots with R and Plot.ly
Appreciated 11 months ago, created a post with more than 5 votes. For Automatic IGV snapshot script
Popular Question 12 months ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?
Popular Question 13 months ago, created a question with more than 1,000 views. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Appreciated 15 months ago, created a post with more than 5 votes. For Automatic IGV snapshot script
Appreciated 16 months ago, created a post with more than 5 votes. For Automatic IGV snapshot script
Student 16 months ago, asked a question with at least 3 up-votes. For How to tell which transcript is the canonical transcript?
Popular Question 19 months ago, created a question with more than 1,000 views. For Creating Interactive Volcano Plots with R and Plot.ly
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