User: frcamacho

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frcamacho190
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190
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United States
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2 days, 11 hours ago
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5 years, 7 months ago
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Posts by frcamacho

<prev • 42 results • page 1 of 5 • next >
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Comment: A: esearch discrepancies using bash commands vs direct esearch command line
... This is also a heads up for those using esearch. The esearch command consumed the entire file (stdin), hence I got output only for the first line. I used `IFS=$'\n'; for next in $(cat file); do ..; done` to get it to work with a file as input. ...
written 4 months ago by frcamacho190
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Comment: C: esearch discrepancies using bash commands vs direct esearch command line
... Thank you Pierre! Updated code and it works! cat test-file.txt | while read p; do echo $p; esearch -db gene -query "$p[Gene name] AND Homo sapiens[ORGN] AND alive[Prop]" | efetch -format tabular > results.txt; done; ...
written 4 months ago by frcamacho190 • updated 4 months ago by RamRS27k
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esearch discrepancies using bash commands vs direct esearch command line
... Hi there, I am using esearch to query symbols within a file against NCBI. I am using the following command cat test-file.txt | while read p; do echo $p; esearch -db gene -query '"$p"[Gene name] AND Homo sapiens[ORGN] AND alive[Prop]' | efetch -format tabular > results.txt; done; In the tes ...
ncbi entrezdirect esearch written 4 months ago by frcamacho190
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Comment: C: Pheatmap or Heatmap3 ?
... I used to use pheatmap, but I agree with @RamRS. ComplexHeatmap brought R heatmaps a needed makeover. You should take a look at the complete reference for ComplexHeatmap to get you started. > https://jokergoo.github.io/ComplexHeatmap-reference/book/introduction.html ...
written 4 months ago by frcamacho190
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Comment: C: prinseq and sickle
... Can you please attach the conda commands you used to run the installation? For example; > `conda install -c bioconda prinseq` Also, any error messages you received. Did you install prinseq and sickle within a conda environment? If so, make sure you are activating your environment before callin ...
written 4 months ago by frcamacho190
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Comment: C: Query UniProt database with Mnemonic identifier
... Update: I was able to convert using http://www.uniprot.org/mapping/ from UniProtKB AC/ID to UniProtKB. This works, but would like to be able to implement some code. Thanks! ...
written 2.0 years ago by frcamacho190
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Query UniProt database with Mnemonic identifier
... I have a list of UniProt Names, Mnemonic identifier of a UniProtKB entry. I am trying to query the UniProt database to retrieve the information of that entry that matches the mnemonic identifier and following filtering: Human taxa and Reviewed. Is there a way to do this in R? What I currently am doi ...
R uniprot written 2.0 years ago by frcamacho190
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Retrieve sequences that generated a HMM profile
... Hi All, I have HMM profiles but the raw sequences or multiple sequence alignments are not available. I saw the tool `hmmemit`, but this randomly generates sequences that match a given profile HMM. I do not want random sequences. Is there a way to obtain sequences or multiple sequence alignment tha ...
hmmer written 2.3 years ago by frcamacho190 • updated 2.3 years ago by Jean-Karim Heriche22k
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Comment: C: Help with CD-hit commands for DNA sequences
... Which version are you running? I am running 4.6 (built on Jul 29 2016) ...
written 3.2 years ago by frcamacho190
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Comment: C: Help with CD-hit commands for DNA sequences
... I thought cdhit -est were not good for large sequences. My max is 71KB large. Is cdhit-est ok? ...
written 3.2 years ago by frcamacho190

Latest awards to frcamacho

Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Continuously add lines to ggplot with for loop
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Tabular fields of DIAMOND.m8 file
Supporter 4 months ago, voted at least 25 times.
Great Question 6 months ago, created a question with more than 5,000 views. For Tabular fields of DIAMOND.m8 file
Great Question 11 months ago, created a question with more than 5,000 views. For Tabular fields of DIAMOND.m8 file
Great Question 11 months ago, created a question with more than 5,000 views. For Conditionally merge columns using Pandas
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Continuously add lines to ggplot with for loop
Epic Question 16 months ago, created a question with more than 10,000 views. For Conditionally merge columns using Pandas
Popular Question 18 months ago, created a question with more than 1,000 views. For Tabular fields of DIAMOND.m8 file
Great Question 2.2 years ago, created a question with more than 5,000 views. For Conditionally merge columns using Pandas
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Tabular fields of DIAMOND.m8 file
Scholar 3.0 years ago, created an answer that has been accepted. For A: Sublime Text 2: Output Error After I Installed Anaconda
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Conditionally merge columns using Pandas
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Conditionally merge columns using Pandas
Popular Question 3.7 years ago, created a question with more than 1,000 views. For parsing hammer 2.3.2 results using biopython
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Bulk downloading IMG gene ID information
Scholar 3.8 years ago, created an answer that has been accepted. For A: Sublime Text 2: Output Error After I Installed Anaconda
Popular Question 3.9 years ago, created a question with more than 1,000 views. For parsing hammer 2.3.2 results using biopython
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Sublime Text 2: Output Error After I Installed Anaconda
Scholar 4.9 years ago, created an answer that has been accepted. For A: Sublime Text 2: Output Error After I Installed Anaconda

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