Moderator: RamRS

gravatar for RamRS
RamRS23k
Reputation:
23,240
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Trusted
Location:
Houston, TX
Twitter:
@_RamRS
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Google Scholar Page
Last seen:
an hour ago
Joined:
6 years, 1 month ago
Email:
r****@nyu.edu

Bioinformatician turned Microsoft technologies developer turned bioinformatician. I love messing with text. UNIX>R>Python>Perl programmer, Excel pro, master Googler, database expert. 

I'm an amateur biologist interested in translational human genetics and healthcare.

Posts by RamRS

<prev • 4,986 results • page 1 of 499 • next >
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Comment: C: Is there a good way to do a PCA of gene expression including samples from differ
... When is the batch effect accounted for in DESeq2? I thought that since the design formula (which includes the batch as a covariate) is specified when the dataset is imported, all operations would take the batch effect covariate into account. Is that assumption mistaken? ...
written 1 hour ago by RamRS23k
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Comment: C: Is there a good way to do a PCA of gene expression including samples from differ
... I understand that most statisticians argue against TPM etc, but the thing is, what other metric would one use? There are cases when one cannot rely on a downstream algorithm to account for other variables, so until we get to an alternative metric - an actual solution - TPM might have to do as the be ...
written 3 hours ago by RamRS23k
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Comment: C: Convert intron coordinates to gene names
... > but I wasn't able to get the desired output. What exactly went wrong? Did you try all the solutions in that thread? ...
written 1 day ago by RamRS23k
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Comment: C: biopython string object
... Find matches to a regular expression + substitute = `re.sub` is the first thing that comes to my mind, as the substitute operation is not complex enough to warrant a find/match followed by a bunch of steps. From a cursory glance at `re` documentation (I don't use python), it seems like the substitut ...
written 1 day ago by RamRS23k
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Comment: C: biopython string object
... If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. ![Upvote|Bookmark|Accept][1] [1]: https://image.ibb.co/dfsqrx/upvote_accept_bookmark.png ...
written 1 day ago by RamRS23k
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Comment: C: biopython string object
... Do you absolutely need to use python? Would it not be easier to just use `sed`? Also, why not use `re.sub(..., count=0)`? ...
written 1 day ago by RamRS23k
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Comment: C: The nucleiotide sequence to gene id
... Please search the site (and generally on Google also) for command line blast. That should help you query sequences in bulk. ...
written 1 day ago by RamRS23k
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Comment: C: The nucleiotide sequence to gene id
... > smth Please do not use Instant Messaging jargon on a scientific/professional forum. If sequence is the only data point to go by, you're going to need to use BLAST to figure out the gene that each sequence aligns to with the highest certainty. It might be worth a shot to contact the someone wh ...
written 1 day ago by RamRS23k
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Comment: C: The nucleiotide sequence to gene id
... Your DESeq2 operation must have used a dataset generated using an RNAseq pipeline that internally used a GTF file. Can you trace the workflow back to the GTF file? ...
written 1 day ago by RamRS23k
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Comment: C: Help please! How do you extract Y-STR data from individual 1000genomes samples?
... What is your scientific hypothesis? How would you reconstruct STR information from variant information? ...
written 1 day ago by RamRS23k

Latest awards to RamRS

Popular Question 2 days ago, created a question with more than 1,000 views. For Benefit of platinum genomes in WGS experiment
Teacher 3 days ago, created an answer with at least 3 up-votes. For C: .slurm vs .sh files
Commentator 4 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics and biotechnology market in future.
Commentator 9 days ago, created a comment with at least 3 up-votes. For C: Help with RNA-seq analysis
Teacher 15 days ago, created an answer with at least 3 up-votes. For C: .slurm vs .sh files
Student 17 days ago, asked a question with at least 3 up-votes. For Metric to use for RNAseq expression matrix
Scholar 17 days ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Teacher 23 days ago, created an answer with at least 3 up-votes. For C: .slurm vs .sh files
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: Help with RNA-seq analysis
Scholar 24 days ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Appreciated 4 weeks ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: How to get gene annotation for a list of genes
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: How to get gene annotation for a list of genes
Scholar 4 weeks ago, created an answer that has been accepted. For C: How to get gene annotation for a list of genes
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: I couldn't install DEseq2?
Scholar 5 weeks ago, created an answer that has been accepted. For C: I couldn't install DEseq2?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: I couldn't install DEseq2?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: I couldn't install DEseq2?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: I couldn't install DEseq2?
Appreciated 7 weeks ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For C: I couldn't install DEseq2?
Scholar 7 weeks ago, created an answer that has been accepted. For C: I couldn't install DEseq2?
Appreciated 7 weeks ago, created a post with more than 5 votes. For Meta: Markdown in Biostars (now enabled)
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For C: I couldn't install DEseq2?
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Help with RNA-seq analysis

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