Questions tagged [public-dataset]
The public-dataset tag has no usage guidance.
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Generating simulated gold standard NGS dataset/ Any publicly available smal gold standard NGS dataset
I am trying to check my variant generation pipeline for humans. The pipeline is for NGS. I am searching for any dataset(.fastq+.bam+.vcf) for any specific sample. Now, GIAB has a nice dataset for that....
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How to access yeast-cyc in a programmatic way to extract the GO terms?
I am a newbie in Bioinformatics, I want to extract the GO terms from yeast-cyc,
which is items in the Go terms tab of this page https://yeast.biocyc.org/gene?orgid=YEAST&id=G3O-29622#tab=GO , not ...
- 113
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consortium, biobank or browser with CNV eQTLs
I found that GTEx contains several SNPs eQTLs, but I'm looking for previously reported CNV-eQTLs, where can I find such data (freely available)?
- 307
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datasets or biobanks with both (WGS or genotype intensity) and methylation data
My aim is to associate CNVs to DNAm, but I don't know where to find datasets which contain both (sequencing + methylation). Do you know any?
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How many protein sequences do we usually have for each species?
My question is exactly the one in the title. I add a particular example for more clarity. If I want to study the sequence of protein IkBα, do I find only one sequence or is there a database that ...
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Integrating bulk RNA-Seq data with different sequencing depths and from different sources
I am attempting to integrate different bulk RNA-Seq datasets. While this is not ideal, I'm trying to reduce the technical variability in these datasets by using data generated by similar protocols (...
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What options should I explore to improve the output of the protein reconstruction?
We developed a neural network-based protein reconstruction tool to reconstruct the main chain from only CA atoms.
we generated data from some selected PDBs from the RCSB website to train an NN model.
...
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Building database for MetaCache takes extremely long
A question to those who have experience with MetaCache (metagenomic tool):
I have tried to build the MetaCache taxonomy from refseq (only bacteria), as described in the EXAMPLES here. However, the ...
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syndip dataset for benchmark variant
I have a question about syndip dataset : https://github.com/lh3/CHM-eval .
I'm struggling to find the syndip vcf.
In the release ( https://github.com/lh3/CHM-eval/releases ), we have a file named : <...
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Database to download with information of bacteria?
I am looking for tidy tabular dataset that contains known bacteria and fungi down to the species level. Basically a table that includes genus and species names and other higher-level information. For ...
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202
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How to get a FASTA format file with the DNA sequences of all annotated genes?
I am analysing Pyrococcus Furiosus DNA sequencing data by considering data published here in NCBI. When I click on "Send to">"Gene Features">"FASTA format" I ...
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How do I download the mitochondrial haplogroup datasets for human genetics online?
I seem to have landed on the mitomap.org site, but I don't know what to make of it or what do with it / how to get the genomes onto my computer. It sounds like the genomes are stored in GenBank, but ...
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Fastq dataset after clustering
I'm doing a project for DNA archival storage systems
Is there an open-source dataset used as ground truth for clustering?
E.g
A file containing the ground truth strand sequences, which have been ...
- 111
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228
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Available phenotype data from GTEx
I am using gene expression data from the The Genotype-Tissue Expression (GTEx) project, available here: http://gtexportal.org. I would also like to use phenotype data for each sample (especially age, ...
- 257
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How to download RNAseq gene expression data from GTEx
I would like to download RNAseq gene expression data from GTEx from the liver only. What is the best way to do this?
I have tried a few things. I downloaded several files from the GTEx website (https:...
- 257
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NA12878 equivalent for somatic variant calling [duplicate]
I'm building a somatic variant calling pipeline with snakemake. The pipeline is hosted on Github, and I'd like to use Travis CI for continuous integration testing. ...
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What are the largest fully publicly available molecular QTL datasets?
I'm familiar with the sQTL and eQTL GTEx data that can be downloaded from the
GTEx Portal, but I'm interested in gathering at least two other types of molecular QTL datasets:
Larger eQTL and/or sQTL ...
- 191
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88
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Appropriate value to replace outliers in clinical studies
I am working on clinical study where I am focusing on binary classification problem.
There are few variables which has outliers.
I am trying to know which would be the right value to replace ...
- 217
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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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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.
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Are there any Genome in a Bottle-like resources for non-humans (especially for invertebrates)?
Genome in a Bottle is an excellent resource that provides many types of DNA and RNA sequencing reads for a single individual/cell line to test genome assembly and analysis tools. For example there are ...
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Recommendation for a binary dataset for Computational Biology open access (as in a dataset with 1 and 0 that can be used to apply ML techniques? [closed]
I have a couple of modified ML methods that I want to test with biological binary data - specifically binary gene expression data - e.g. https://eprints.soton.ac.uk/69359/1/Thesis.pdf that might ...
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Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?
I am not sure whether this is the best SE community for this question.
I want to publish a transcriptome paper, along with interactive materials enabling readers to peruse the data behind the ...
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Is there a publicly available tumor-normal sample?
I am looking for a publicly available matched tumor-normal sample. I need Illumina fastq reads (or an aligned bam file, since I could extract the reads from it) from a tumor and a matching, non-tumor ...
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