Questions tagged [data-retrieval]
The data-retrieval tag has no usage guidance.
25
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Sql query slow on Chembl postgres database
Doing complex sql query on Chembl database and it takes 40 minutes on the machine from lab.
I was thinking using dask, extract each table and export to parquet, when do the data processing .
Is this a ...
- 13
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2
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304
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Where can I find examples of published bioinformatics pipeline packages? [closed]
I am a software engineer and I am preparing a presentation to aspiring bioinformatics PhDs on how to use best-practice software engineering when publishing code (such as include documentation, modular ...
- 121
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3
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73
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eQTL data extraction from database JSON file
I have a long list of JSON data, with repeats of contents similar to followings.
Due to the original JSON file is too long, I will just shared the hyperlinks here. This is a result generated from a ...
- 13
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28
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Do proper .fcs flow-cytometry files specify the gating hierarchy, so one may calculate cell-counts without specifying it themselves?
Do proper .fcs flow-cytometry files already have the gating hierarchy, so one may calculate cell-counts without extra work?
https://github.com/whitews/FlowKit/
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39
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querying gdc metadata issues with resulting fields
I have been trying to access metadata from the Genomic Data Commons; however, not all of the information I want is showing up in the resulting tsv file. How do I get sample type and analyte type to ...
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81
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Print specific columns in a matrix on the basis of sample id's in the header
I have a matrix file (expression.txt) in which the first column is a gene_id and from the second column the sample id's start. This matrix has 20,000 columns with sample id's corresponding to ...
- 351
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11
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Drug classification database information
Is there any database that give information about the drug class. Right now I have all the MeSH id of the drugs from different publications. So right now I'm looking one by one drug looking at the ...
- 1,754
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4
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518
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How can I obtain FTP links to studies in ENA given a BioProject ID?
How can I programmatically obtain ftp links to RNA seq fastq files in ENA? Here's an example of a link that I would be interested in obtaining:
...
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Are there databases or resources that contain expression of proteins or genes before and after cancer treatment?
Are there databases that contain information about gene or protein expression before and after targeted therapy or chemotherapy?
I am curious about different cancer cell lines or cancer types.
Any ...
- 1,427
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470
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Raw Data frame manipulation in python
Using python 3 I need to process qPCR sequencing raw data outputs by searching for the first occurrence of a user defined string and then making a new data frame using all lines after that string. I ...
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48
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NCBI retrieve genome assembly with splicing or "modifications"
I am trying to fetch genome assemblies that include splicing information.
E.g. Here, is a genome assembly of a yeast, where genes show variants like this: ...
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48
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Retrieving Metabolic networks from WIT Database
How can I get the dataset for all the 43 metabolic networks for this paper:
https://www.nature.com/articles/35036627
It looks like the WIT database does not exist anymore.
- 15
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213
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List of human transcription factors
I'm looking for a list of human transcription factor (TF) genes.
Where can I find a TF database or how can I retrieve this list from other databases?
- 2,624
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228
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GDC data portal cancer subtype
I need to use Gene Expression quantification data (using HTSeq-FPKM-UQ) for breast cancer data on the gdc portal (https://portal.gdc.cancer.gov/repository) to classify breast cancer subtypes (luminal ...
- 11
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46
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Where to download baseline/average gene expression level of all human coding genes?
I am looking for the most appropriate dataset for downloading baseline gene expression level across all human coding genes during development. I am aware that EMBL Expression Atlas is one of the ...
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Blueprint replicates
On Encode, it's pretty easy to find out replicate information about the experiments, however I am having some difficulty finding this information on BLUEPRINT DDC, at http://dcc.blueprint-epigenome.eu
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Viral Load and Antiretroviral Therapy Dataset
My project is on Mathematical Modeling of the relationship between viral load and antiretroviral therapy. Its purely an academic investigation which is exploratory in nature.
Question I am seeking a ...
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CRISPR Sequence Finder and Database Download
I am searching for tools to pull CRISPR Spacers from Bacterial Genomes. I am aware of the CRISPRDB and the corresponding identification tool on the web server.
Are there other tools for finding ...
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NCBI - edirect suite to download all genome sequences associated with a query - troubleshooting
Not sure if this is allowed but I cannot think of a better place to ask. I am attempting to download all genomic sequences from refseq associated with the query Peptostreptococcaceae. I have been been ...
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1
answer
64
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Automating sequence download from Wormbase
I'm working on the C. elegans model organism, for which there exists an online biological information database: Wormbase.
I'm able to manually search for a transcript (say "K06C4.12") and this gets ...
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729
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Retrieve abstract/summary for NCBI bookshelf via Entrez
I want to retrieve abstracts/summaries for NCBI bookshelf entries, eg: "NBK1440"
Docs say the dbname is "books" and efetch guide says a rettype of "docsum" works for all databases. However when I ...
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191
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How to access organism IDS, taxon nodes from UniProt?
I try to find organism IDs used by UniProt (e.g. 9606 for "Homo sapiens") and information about the 'taxonomic kingdom' this organism belongs to. The only source on UniProt I could find is this file ...
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893
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How to interconvert InChI and InChIKey?
I would like to retrieve IDs from several databases using InChI as an input, e.g.
...
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3
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513
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How to retrieve InChI key for KEGG compound?
I would like to retrieve the InChI representation for a given KEGG compound but I fail to find a direct solution for this (preferably doing it via bioservices).
One could do it via ChEBI like this:
...
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216
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How to retrieve logical expressions (KO based) for reactions from KEGG?
The completeness of a module can easily be checked by looking at the Definition entry associated with the module. For example, in module M00010, it is given as:
<...
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