Top new questions this week:
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I was wondering if there is more elegant way of installing and loading multiple packages in Bioconductor similar to pacman with CRAN packages.
I tried:
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Are there best practices of loading different bioinformatics file formats such as VCF, BED, and GFF to an SQL database? I am wondering how people out there do that efficiently.
All of these three ...
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Can some explain why when I run a REST API query on UniProt for one ID ('Q9UJL9'), the results for three IDs are returned?
The query I'm using is:
https://www.uniprot.org/uniprot/?query=Q9UJL9&...
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Say I found an interesting protein in a genbank file, e.g.:
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I have a fastq file of 400,000 reads (so speed is important). In the sequences there are barcodes integrated that should be present twice. Given a barcode, I want to find the sequences that have the ...
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I want to retrieve all overlaps between two sets of genomic intervals (GRanges) using Bioconductor. I am interested in the widths of the resulting overlapping ranges.
In cases with discontinuous ...
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Greatest hits from previous weeks:
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FeaturePlot is a function in Seurat package.
And in the vignette it is written that if we specify parameter do.return = TRUE it ...
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My colleague and I have developed a software tool intend to release it open-source. This tool is specifically for tasks in bioinformatics but we think it would be helpful for the wider community. Our ...
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In this answer, it is stated that ribosomal genes should be excluded prior to normalization in scRNA-seq as contaminants.
Do mitochondrial genes have to be excluded as well? I plotted the top 50 ...
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I'm very new to bioinformatics in general, and I'm trying to understand some basic concepts.
I have RNAseq data, and bioinformatics people tell me that intensities cannot be compared across patients. ...
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What is the index fastq file that comes with some Illumina sequencing datasets? (The samplename_I*.fastq.gz file.)
For example, I recently received some 10X ...
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I have a fasta file like this:
>Id1
ATCCTT
>Id2
ATTTTCCC
>Id3
TTTCCCCAAAA
>Id4
CCCTTTAAA
I want to delete sequences that have the following IDs.
<...
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I would like to convert a BED format to GFF3.
The only useful tool that I could find via a google search seems to be Galaxy, ...
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