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3 votes
Accepted

Is there a publicly available tumor-normal sample?

Please take a look at An open access pilot freely sharing cancer genomic data from participants in Texas Although I have not worked on this paper but author claimed that both tumor and normal data ...
Lot_to_learn's user avatar
3 votes

Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?

You may try Code Ocean. Currently, it is not that easy to use IMHO, but one of their tech leads promises to substantially improve it towards the year end.
user172818's user avatar
  • 6,535
3 votes
Accepted

Available phenotype data from GTEx

If helpful for anyone else, I found that all and much more are available. See below 2 links. https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/dataset.cgi?study_id=phs000424.v8.p2&phv=169091&...
Sylvia Rodriguez's user avatar
3 votes

Appropriate value to replace outliers in clinical studies

In my experience, it is more common to use all clinical data as-is for clinical studies. And if data is missing, either omit the sample or omit the variable with missing data. If your classifier can'...
Reilstein's user avatar
  • 367
2 votes
Accepted

Are there databases or resources that contain expression of proteins or genes before and after cancer treatment?

One such database/tool is “[PharmacoGx][1]: an R package for analysis of large pharmacogenomic datasets.” Bioinformatics (Oxford, England). They brought together a ...
haci's user avatar
  • 4,142
2 votes
Accepted

Retrieving Metabolic networks from WIT Database

It seems like there are some files related to the databases at the ftp site: http://ftp.mcs.anl.gov/pub/WIT2/. The related files were last updated on 2002. I found it via searching at google: ...
llrs's user avatar
  • 4,713
2 votes
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Are there any Genome in a Bottle-like resources for non-humans (especially for invertebrates)?

In addition I would like to add "Vectorbase", the curator "Dan" is a good guy (I forget his surname right now) and it's a good team. However, please read my rather somber assessment of arthropod ...
M__'s user avatar
  • 12.5k
2 votes

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?

Kaggle has a cats v dogs dataset if you want to try your hand at biological image classification: https://www.kaggle.com/c/dogs-vs-cats The DREAM challenge competitions are usually specifically ...
Jay Moore's user avatar
  • 1,012
2 votes

How many protein sequences do we usually have for each species?

I'm going to start by assuming that you don't actually want 10 protein sequences from the same species, even though you write this in your comment on M__'s (deleted) answer. This will not be a very ...
Maximilian Press's user avatar
2 votes

Integrating bulk RNA-Seq data with different sequencing depths and from different sources

Per-sample coverage / count differences are expected in all differential expression analysis, and correction for that is built into DESeq2. You shouldn't need to do any additional correction with ...
gringer's user avatar
  • 14.3k
2 votes

Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?

I have seen some (1 or more) articles with interactive data displays in the F1000Research journal I don't know recall now if they had interactive tables or plots but they used plotly for sure.
llrs's user avatar
  • 4,713
2 votes

Generating simulated gold standard NGS dataset/ Any publicly available smal gold standard NGS dataset

I would suggest subsampling an existing dataset such as the GIAB resource that you've already indicated. Use a utility such as seqtk to subsample the appropriate number of reads from the dataset, and ...
Maximilian Press's user avatar
1 vote

Is there a database of oligonucleotide duplex sequences and their melting temperatures

Not exactly what you're asking, but the modeling program/API ViennaRNA has excellent and accurate utilities for predicting the stability ($\Delta \Delta G$ of folding) for arbitrary oligonucleotide ...
Maximilian Press's user avatar
1 vote
Accepted

How to access yeast-cyc in a programmatic way to extract the GO terms?

You can get the GO terms for yeast from UniProt, e.g. https://uniprot.org/uniprotkb?query=(taxonomy_id:559292). Using the UniProt website you can generate an API endpoint URL for your query, e.g. here ...
jared_mamrot's user avatar
1 vote
Accepted

How many protein sequences do we usually have for each species?

Just to add to Maximilian Press's answer. I happen to know about human immunology and I think Maximilian Press has a good idea. Genetic studies and immunological studies per se in cellular immunology ...
M__'s user avatar
  • 12.5k
1 vote

Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?

The example looks a lot like a shiny application. Your best bet then is one of the following: Ask your IT department to setup a shiny server for you. They can use the free version. Post your shiny ...
Devon Ryan's user avatar
  • 19.6k
1 vote
Accepted

What options should I explore to improve the output of the protein reconstruction?

The first step is to assess the accuracy, recall and precision of the model then look at confusion matrix. Thereafter consider ROC AUC and if all those are fine ... it's biological. If the model is ...
M__'s user avatar
  • 12.5k
1 vote
Accepted

syndip dataset for benchmark variant

If you want the truth VCF, it is full.37m.vcf. rep2.37.broad.hc.raw.vcf.gz is an example call set by GATK.
user172818's user avatar
  • 6,535
1 vote

Database to download with information of bacteria?

You can try Entrez in Biopython. Although, there is hassle with additional information. ...
Vovin's user avatar
  • 435
1 vote

How to get a FASTA format file with the DNA sequences of all annotated genes?

From this SO post. You can use seqkit to remove duplicate sequences with the command below: seqkit rmdup -s < sequences.txt > out.fa The ...
Throckmorton's user avatar
1 vote

How do I download the mitochondrial haplogroup datasets for human genetics online?

Hmmm, I am not experienced enough in biology or bioinformatics to truly understand the question, but I am guessing you want to download the FASTA file or genebank file containing the sequence of the ...
Neeleshwar Pandey's user avatar
1 vote
Accepted

How to download RNAseq gene expression data from GTEx

Gene read counts are the number of reads or fragments that are mapped to each gene. So it is an integer and the values are not directly comparable between samples due to differences in sequencing ...
Phoenix Mu's user avatar
1 vote

What are the largest fully publicly available molecular QTL datasets?

The largest eQTL datasets I can think of is probably eQTLGen. This is a meta-analysis of many studies using >30,000 samples from whole blood. This might be less ideal if you want cell-type-specific ...
Phoenix Mu's user avatar
1 vote

Appropriate value to replace outliers in clinical studies

Removing outliers is common practice in statistical modeling and perfectly acceptable. However, with regards 1.5 IQR I am far from certain about this approach. Normally, if you want to be conservative ...
M__'s user avatar
  • 12.5k

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