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2 votes
1 answer
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Is there a database of oligonucleotide duplex sequences and their melting temperatures

I am looking for melting temperatures of oligonucleotide duplexes, but I am having trouble finding data. Can be DNA-DNA, DNA-RNA, or RNA-RNA duplexes, native or modified nucleotides.
biologist774's user avatar
0 votes
0 answers
16 views

ZINC15 database: proxy server error when trying to download catalog in any format

I am a complete beginner in the use of such databases. When navigating to the ZINC15 database website and trying to download an entire catalog with the "Download all as" option the request ...
Zea Mays's user avatar
0 votes
0 answers
8 views

Where would I get the activity profile dataset for Lantus Solostar insulin, and for other diabetes treatments such as Metformin?

I am working on a personal project for a better, more informed management of my own Diabetes Mellitus, Type 2 (aka "T2DM", or "T2D"). With some difficulty I am able to access and ...
Fritt Ro's user avatar
-1 votes
1 answer
35 views

Where can you download functional domain labels of the human genome?

I'm visualizing where mutations occur in a gene, and would like to add functional domains to the plots. I have some trouble locating sources to download data on functional domains. The dataset should ...
Sofie's user avatar
  • 1
0 votes
1 answer
30 views

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....
Shafayet Rahat's user avatar
1 vote
1 answer
32 views

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 ...
Mountain's user avatar
  • 113
2 votes
0 answers
15 views

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)?
Caterina's user avatar
  • 307
2 votes
0 answers
15 views

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?
Caterina's user avatar
  • 307
1 vote
2 answers
110 views

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 ...
HelpNeederStudent's user avatar
5 votes
2 answers
949 views

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 (...
CodingSquirrel's user avatar
1 vote
1 answer
46 views

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. ...
user366312's user avatar
2 votes
0 answers
29 views

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 ...
Roger V.'s user avatar
  • 381
0 votes
1 answer
70 views

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 : <...
Maryem Life's user avatar
1 vote
1 answer
43 views

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 ...
Soerendip's user avatar
  • 1,295
0 votes
1 answer
216 views

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 ...
HelpNeederStudent's user avatar
2 votes
1 answer
79 views

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 ...
Lance's user avatar
  • 143
1 vote
0 answers
32 views

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 ...
Brian Formento's user avatar
1 vote
1 answer
242 views

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, ...
Sylvia Rodriguez's user avatar
2 votes
1 answer
1k views

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:...
Sylvia Rodriguez's user avatar
2 votes
0 answers
47 views

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. ...
Tomas Bencomo's user avatar
0 votes
1 answer
60 views

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 ...
CloudyGloudy's user avatar
1 vote
2 answers
100 views

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 ...
The Great's user avatar
  • 227
1 vote
1 answer
45 views

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 ...
0x90's user avatar
  • 1,437
1 vote
1 answer
48 views

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.
ERSA's user avatar
  • 15
4 votes
1 answer
72 views

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 ...
conchoecia's user avatar
  • 3,181
-3 votes
1 answer
144 views

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 ...
user4078's user avatar
2 votes
3 answers
63 views

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 ...
Scientist's user avatar
  • 111
3 votes
1 answer
590 views

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 ...
terdon's user avatar
  • 10.2k