User: benformatics

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benformatics1.6k
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Posts by benformatics

<prev • 174 results • page 1 of 18 • next >
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Comment: C: Order assignment given family and genus level in R
... Do you manually want to add the information? Or are you asking if there is a package that can associate genus to order for you? ...
written 6 weeks ago by benformatics1.6k
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Comment: C: filter_vep not properly filtering
... Why are you using '= delterious' and then 'match damaging' ... I would imagine the system requires some consistency? ...
written 7 weeks ago by benformatics1.6k
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Comment: C: How to quickly tell the reference allele given chr, pos, A1 and A2 allele?
... How are you defining reference here? The one with the highest AF? The reference/alt allele for a given sample isn't necessarily in the reference genome. ...
written 7 weeks ago by benformatics1.6k
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Answer: A: Read genotype information with VariantAnnotation
... This is pretty well illustrated in [the manual][1]... Most standard entries can be accessed using the `info()` or `geno()` function call. I don't think you are going to be able to simply `cbind` all this information together without checking the format of each of the different columns you want to ap ...
written 7 weeks ago by benformatics1.6k
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Comment: C: GGplot2 coord flip problem
... The example dataset in your post works fine for both scripts - if you can't see the bars you probably need to make the display window larger. ...
written 10 weeks ago by benformatics1.6k
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Answer: A: GGplot2 coord flip problem
... Does converting the underscores to new-lines help? my_data_C2C1$Pathway <- gsub("_","\n",my_data_C2C1$Pathway) ...
written 10 weeks ago by benformatics1.6k
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Answer: A: Finding the Refseq Soft-masked Regions
... To solve this I used the script from [steve][1] found here: https://www.biostars.org/p/209383/ using the pattern `[agct]`. The square brackets are standard for python regex and allow for matching to one of any of the characters within the brackets. The script is used to find the index of all matche ...
written 10 weeks ago by benformatics1.6k
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Comment: C: Finding the Refseq Soft-masked Regions
... I'm looking at human data (hg38) but this is probably not super relevant to the question ...
written 11 weeks ago by benformatics1.6k
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Finding the Refseq Soft-masked Regions
... I noticed that in IGV there are **lower case regions (soft-masked).** I want to exclude these in an analysis and was wondering if there was a**n annotation for the sites** that are soft-masked. Like a **bed** file or **GTF** with all the specific soft-masked locations. I could go through and identi ...
refseq igv written 11 weeks ago by benformatics1.6k • updated 10 weeks ago by vkkodali2.0k
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Answer: A: What is the best way to analyze and enrich a list of DE genes from RNAseq?
... In regards to choosing candidates to validate. My suggestion on this end is to accept the following “nothing is consistent”. My suggestion would be to PCR genes with the highest fold-change. If you have to subset from your original list I would still suggest the same. Here is an easy site to use f ...
written 3 months ago by benformatics1.6k

Latest awards to benformatics

Appreciated 9 weeks ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Scholar 10 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 4 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 4 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Scholar 5 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
Scholar 6 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Scholar 7 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 8 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Appreciated 10 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Concept behind p-value correction?
Scholar 11 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Guru 11 months ago, received more than 100 upvotes.
Scholar 11 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: ATAC-seq peak calling with MACS
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Scholar 11 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Appreciated 12 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Popular Question 12 months ago, created a question with more than 1,000 views. For ".1" being appended to Ensembl Gene IDs from UCSC txdb (dm6)
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