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Home Page: http://www.biochat.ai
License: MIT License
Natural language processing of Gene Expression Omnibus data
Home Page: http://www.biochat.ai
License: MIT License
Just keep "Same sequencing type" in the "Choose additional filters:" section, and rename "Look only in these library strategies" into "Look only in these sequencing types".
GSE21304 is a study for methylation profiling by array, but the Sequencing type is showing other
in the Biochat web app.
Why is the code indentation like it is? Is an automatic indenting editor used?
Just question.
Or just read the "Why Lisp?" section at: http://biolisp.org
Can't access biolisp.org
Most of the GDS entries are "Technology type: in situ oligonucleotide", which means it's a microarray sample. We should add this to the metadata field. Just scrape the Technology type
metadata field for all GDS entries and replace "in situ oligonucleotide" with "microarray" in the UI.
Going to https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS651 and clicking on the hyperlinked GPL570 leads to a page that says: "Technology type: in situ oligonucleotide" which should be coded as microarray. Currently, GDS651 returns Sequencing type: other
, whereas it should be microarray
.
Remove the "SELEX", "WGS", and the empty artifact. Check how many records are in SELEX and WGS first before removing and post this info here (with a date/timestamp when you retrieved these records).
Replace the capitalizations and change to nicely formatted:
"Microarray", "Bisulfite-seq", "ChIP-seq", "RNA-seq", "RIP-seq", "DNase-seq", "ATAC-seq", "miRNA-seq", "MNase-seq", "Tn-seq", "FAIRE-seq", "MeDIP-seq", "ncRNA-seq", "MRE-seq", "MBD-seq", "Hi-C", "ssRNA-seq", "FL-cDNA"
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