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 ...
- 560
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.
- 6,485
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&...
- 257
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'...
- 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 ...
- 3,947
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: ...
- 4,693
2
votes
Accepted
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__♦
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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 ...
- 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 ...
- 3,794
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 ...
- 13.8k
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.
- 4,693
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 ...
- 3,794
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 ...
- 695
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__♦
- 11.9k
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 ...
- 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__♦
- 11.9k
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.
- 6,485
1
vote
Database to download with information of bacteria?
You can try Entrez in Biopython. Although, there is hassle with additional information.
...
- 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 ...
- 810
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 ...
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 ...
- 857
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 ...
- 857
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__♦
- 11.9k
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