User: steve

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steve1.8k
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Posts by steve

<prev • 215 results • page 1 of 22 • next >
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Comment: C: merging data frames in r
... column names do not need to be sorted, they only need to exist in both dataframes. `rbind(df1, df2)` would return a new dataframe with the rows of `df2` appended to the bottom of `df1` ...
written 2 hours ago by steve1.8k
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Comment: C: Overlapping SNPs in R
... Assuming you have variants loaded into a dataframe in R in the format of Chrom Pos Ref Alt, I typically do this by making a new column in the dataframe where I concatenate those fields into a single text string. Then I make a new `list` out of such columns for all the datasets I am overlapping, and ...
written 2 hours ago by steve1.8k
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Comment: C: Database for longterm storage of genomic data
... dont put them in a database. Put them somewhere on the server and store paths to the files in the database. ...
written 2 days ago by steve1.8k
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Comment: C: Conda on MacOS
... why are you using `curl` instead of the `wget` command you posted? ...
written 25 days ago by steve1.8k
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Comment: C: How can I make a .bed file from my fasta?
... It sounds like your trouble is in the bamtobed step. I would focus on troubleshooting that. Might want to check the .sam output to make sure it actually has content and that the alignment worked. ...
written 25 days ago by steve1.8k
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Comment: C: How To Produce Simulated 'Synthetic' Sequences
... I found this tool which sounds similar to what you are looking for: [bamsurgeon](https://github.com/adamewing/bamsurgeon). Havent tried it yet though ...
written 27 days ago by steve1.8k
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Comment: C: Why I can not install anything on R?
... if you just updated your Mac, you may have to open Xcode and click some buttons to enable all developer tools, or check for Xcode system updates ...
written 29 days ago by steve1.8k
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Comment: C: Why I can not install anything on R?
... you have to activate `conda` first. You should do this from the directory that you installed `conda` into. The command is usually `source conda/bin/activate`. To deactivate it, you would run `source deactivate` ...
written 4 weeks ago by steve1.8k
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Comment: C: Why I can not install anything on R?
... Assuming you are on a Mac or Linux system (appears to be Mac based on your error messages), you don't actually have to mess with any Python stuff to do this if you install `conda` in batch mode; the command would look something like this: `wget https://repo.continuum.io/miniconda/Miniconda3-latest-M ...
written 4 weeks ago by steve1.8k
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Answer: C: Why I can not install anything on R?
... As an alternative, you might try installing R into `conda` instead (full Anaconda download [here](https://www.anaconda.com/download/#macos), slimmed down Miniconda download [here](https://conda.io/miniconda.html)). This has become my preferred method of installing R and its packages, since it is muc ...
written 4 weeks ago by steve1.8k

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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
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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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Popular Question 8 months ago, created a question with more than 1,000 views. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
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Popular Question 17 months ago, created a question with more than 1,000 views. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
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