User: benformatics

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benformatics1.4k
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ETH Zurich
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Posts by benformatics

<prev • 150 results • page 1 of 15 • next >
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Comment: C: How to draw a figure which is a large circle containing many differently sized c
... The figure in question was likely generated from multiple plots combined using something like Adobe Illustrator. ...
written 7 days ago by benformatics1.4k
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Answer: A: How to draw a figure which is a large circle containing many differently sized c
... If you are able to use R, this can be done with [ggraph][1]. [1]: https://ggraph.data-imaginist.com/articles/Layouts.html#hierarchical-layouts ...
written 7 days ago by benformatics1.4k
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Comment: C: ssGSEA from R and Gene Pattern with Heatmap from Gene Pattern
... Please include some code snippets and the errors produced. A `head()` of whatever data object is being fed into each program would also be helpful. Without any of this, answering your question is near impossible. As to your second part, popular options for making heatmaps from data.frame's in R are ...
written 8 days ago by benformatics1.4k
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Comment: C: The rate of "aligned concordantly exactly 1 time" in Hisat2
... Why did you remove 10 nt from the start of the read? This was clearly unnecessary as HISAT2 will soft-clip alignments when needed - unless otherwise specified. Your alignment rate is very good in the first place. It could be that you trimmed your reads too short and now they multi-map. ...
written 13 days ago by benformatics1.4k
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Comment: C: Downloading 3' UTR sequences for miRNA Target Prediction
... How do you know that these genes even have 3'UTRs? ...
written 14 days ago by benformatics1.4k
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Answer: A: Interesting things to do with 23andme data
... You can [convert your results into a VCF][1] and then plug them into [Ensembl VEP][2] but then take a look at the nonsense/missense mutations that affect protein coding genes. However, I would take the results with a grain of salt. [1]: https://samtools.github.io/bcftools/howtos/convert.html [ ...
written 14 days ago by benformatics1.4k
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Comment: C: how to get gene symbol from Entrez id
... That is still the unfiltered data.frame. You would need to include: `filters="entrez_gene_id"` in your `getBM()` call for it to only use your ids. ...
written 14 days ago by benformatics1.4k
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Comment: C: how to get gene symbol from Entrez id
... I fixed it already now you get everything ...
written 14 days ago by benformatics1.4k
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Answer: A: how to get gene symbol from Entrez id
... library(biomaRt) ## change your dataset if necessary below mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl")) ## return data.frame of all genes with both their entrez ids and gene symbols (some genes have no entrez id) dataframe.genes <- getBM(attributes ...
written 14 days ago by benformatics1.4k
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Answer: A: CPM or TPM in GSEA analysis
... For most intents and purpose **TPM is superior to CPM** (at least for short read RNA-seq; where the length of a given transcript affects the number of reads produced from said transcript). However, CPM should give comparable results to using TPM. In your case, I would try both and compare the result ...
written 19 days ago by benformatics1.4k

Latest awards to benformatics

Scholar 21 days ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 11 weeks ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Scholar 3 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 3 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Appreciated 6 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Concept behind p-value correction?
Scholar 6 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Guru 6 months ago, received more than 100 upvotes.
Scholar 6 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: ATAC-seq peak calling with MACS
Centurion 7 months ago, created 100 posts.
Scholar 7 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Appreciated 8 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Popular Question 8 months ago, created a question with more than 1,000 views. For ".1" being appended to Ensembl Gene IDs from UCSC txdb (dm6)
Scholar 9 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 9 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Subset of genes with at least 1 intron larger than 5000 kbp

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