Gene Expression Omnibus Evaluation
Budget: $250 – $750 USD
I'm currently in need of some specialized assistance in the verification of several GEO (Gene Expression Omnibus) studies. Specifically, I have a list of these studies that require a detailed review to determine whether they meet certain predefined criteria.
By hand, this task should take approximately three-four hours to complete, based on my own experience. However, the time needed may vary depending on your familiarity and comfort level with this kind of work. I do not know how long it would take to automate.
Looking for either MS/PHD level scientist to evaluate by hand or a coder able to develop this description:
As an example, the first item on my list is GSE157103. First, I need to look it up in GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157103) for the words (PBMC, leukocyte, buffy, monocyte, etc.). If found then TRUE. Second, identify the ‘SRA Run Selector’ link on the GEO page and evaluate the SRA. On the SRA Run Selector Page (https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA660067&o=acc_s%3Aa), identify if LibraryLayout = PAIRED, and ‘Sample_type’, ‘source_name’, or ‘cell_type’ equals (PBMC, leukocyte, buffy, monocyte, etc.). If all TRUE, then append a list (csv, xlsx, etc) with the information gathered.
By hand, this task should take approximately three-four hours to complete, based on my own experience. However, the time needed may vary depending on your familiarity and comfort level with this kind of work. I do not know how long it would take to automate.
Looking for either MS/PHD level scientist to evaluate by hand or a coder able to develop this description:
As an example, the first item on my list is GSE157103. First, I need to look it up in GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157103) for the words (PBMC, leukocyte, buffy, monocyte, etc.). If found then TRUE. Second, identify the ‘SRA Run Selector’ link on the GEO page and evaluate the SRA. On the SRA Run Selector Page (https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA660067&o=acc_s%3Aa), identify if LibraryLayout = PAIRED, and ‘Sample_type’, ‘source_name’, or ‘cell_type’ equals (PBMC, leukocyte, buffy, monocyte, etc.). If all TRUE, then append a list (csv, xlsx, etc) with the information gathered.