Moderator: igor

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igor7.6k
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Posts by igor

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Comment: C: How can I do in GTAK downstream analysis?
... You should consider changing your question to the actual problem you are having, which is "find the genes that may causes the disease". GATK helps you get mutations, but it will not help you with understanding them. ...
written 5 days ago by igor7.6k
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Comment: C: bowtie (1) 0% alignment on paired-end RNAseq data
... What if you try to align R1 or R2 independently? There might be an issue with insert sizes. ...
written 8 days ago by igor7.6k
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Comment: C: How to create a heatmap of RNA-Seq Data in R?
... You probably want to use a table of expression values, not stats. ...
written 13 days ago by igor7.6k
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Comment: C: DESeq2: unable to allocate memory error
... Yes, link rot is a problem. Luckily, Google still exists. ...
written 14 days ago by igor7.6k
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Answer: A: Binary mutation data format
... I think the matrix you are looking for can be found at [Xena gene level non-silent mutations][1]. [1]: https://xenabrowser.net/datapages/?dataset=mc3.v0.2.8.PUBLIC.nonsilentGene.xena&host=https%3A%2F%2Fpancanatlas.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443 ...
written 15 days ago by igor7.6k
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Comment: C: scRNA-seq, SEURAT, NormalizeData, ScaleData, PCA, CCA ...
... I edited the statement to make it more clear. I originally meant that all genes (as opposed to all cells) are scaled, but I can see how it can be interpreted in a different way. ...
written 15 days ago by igor7.6k
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Comment: C: Middle author, but not first author projects. How would you approach this?
... Don't you have to be invited for a review? Or are we talking about different reviews? ...
written 16 days ago by igor7.6k
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Comment: C: Middle author, but not first author projects. How would you approach this?
... Is it politically correct to write a sole author paper while in someone else's lab? In this particular case, the author is relatively new to bioinformatics. It sounds like he does not have any publications (even middle author). How do you get a review in that position? ...
written 16 days ago by igor7.6k
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Comment: C: Download hundreds of genes' variant csv from gnomAD
... If you are interested in specific genes, you would probably want to use gnomAD exomes, not genomes. It's based on more samples and the file is substantially smaller. ...
written 17 days ago by igor7.6k
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Comment: C: Is there a tutorial on pathway enrichment analysis in R without ready-made packa
... > someone's interest organism is might not be covered by these tools There are many tools that will work for any organism. > I am interested in figuring out this stuff myself If you have already found some tools, check their source code, which should be available for most of them. ...
written 17 days ago by igor7.6k

Latest awards to igor

Good Answer 7 days ago, created an answer that was upvoted at least 5 times. For A: read length of sequence
Scholar 15 days ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Popular Question 16 days ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Oracle 20 days ago, created more than 1,000 posts (questions + answers + comments).
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Great Question 7 weeks ago, created a question with more than 5,000 views. For Faster BLAST alternative
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Student 7 weeks ago, asked a question with at least 3 up-votes. For smoothing or binning bigWig file
Scholar 7 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: read length of sequence
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Scholar 12 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: GL000201,GL000202... etc What are these?
Popular Question 3 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Popular Question 3 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Scholar 3 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: GL000201,GL000202... etc What are these?
Popular Question 3 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Scholar 3 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Popular Question 3 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: GL000201,GL000202... etc What are these?

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