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10 votes
Accepted

Is there any publicly available multi-omics dataset?

There is a database called OmicsDI, where one can search for multi-omics datasets. Here's a link of the associated publication (Perez-Riverol, Yasset, et al. "Omics Discovery Index-Discovering and ...
user345394's user avatar
5 votes

Given a transcription factor, what genes does it regulate?

MSigDB has a collection (C3:TFT) of gene sets corresponding to transcription factor targets. Harmonizome has functional terms for genes extracted from over a hundred publicly available resources.
burger's user avatar
  • 2,199
4 votes

Given a transcription factor, what genes does it regulate?

In general, there is two options to identify targets for transcription factors: experimental (ChIP-seq) and sequence-based predictions. TF binding from experimental data The are multiple projects ...
Michael Schubert's user avatar
4 votes

Given a transcription factor, what genes does it regulate?

iRegulon takes a sequence-based approach to finding transcription factor targets. There's a Cytoscape app that you can use to find the regulators of a given gene list, or the targets of a particular ...
sjcockell's user avatar
  • 861
3 votes

Is there any publicly available multi-omics dataset?

There are several datasets available on GEO, though you do have to search for them. For example, here are three data sets that have both Illumina methylation and gene expression microarray profiling: ...
user2368936's user avatar
2 votes

Is there any publicly available multi-omics dataset?

Next to OmicsDI the EBI has a special repository for multi-omics datasets: https://www.ebi.ac.uk/biosamples It links the different datasets between repositories, ie. PRIDE for MS/MS based data and ...
Johannes Griss's user avatar
2 votes
Accepted

Software for microbial profiling from 16S rRNA gene sequence

I tried dada2 and is not bad (if you know R). QIIME2 is also an option. Many other are available, the choice might also depend on your sample and your exact question. For functional profiling you ...
Fabio Marroni's user avatar
2 votes
Accepted

Integrative analysis of omics studies using machine learning

The steps you describe are correct. For step 2 it is usually normalized to mean 0 and variance 1. However the "machine learning" part is important. Having several samples being technical replicates ...
llrs's user avatar
  • 4,713
2 votes

Methylation data: beta values are normally distributed

$\beta$ values are the ratio of methylated to unmethylated probe intensities. This means that $\beta \in [0, 1]$, so it can't be normally distributed, by definition. Its distribution may have sections ...
James Hawley's user avatar
  • 1,384
2 votes

Analyzing proteins based on sequence similarity

I suggest you give DAVID a try. Specifically, their Functional Annotation tool. Just enter your list of protein IDs, and it will return groups of proteins where particular GO functions are ...
terdon's user avatar
  • 10.2k
1 vote

How to calculate cell type percentage in every sample

The following package performs this type of analysis and can be directly used on a Seurat object: paper: propeller: testing for differences in cell type proportions in single cell data github: Speckle ...
Macintosh's user avatar
  • 160
1 vote

How to calculate cell type percentage in every sample

If your cell types and sample names are in separate metadata variables attached to the Seurat object, then you can use table to count up the pairings: ...
gringer's user avatar
  • 14.3k
1 vote

Software for microbial profiling from 16S rRNA gene sequence

For comprehensive microbial profiling of your 16S rRNA gene sequence data from Illumina MiSeq, I recommend using the web app Microbioma16S (www.microbioma16s.it). This powerful tool offers an end-to-...
cami's user avatar
  • 11
1 vote

How to combine multiple kernels of large sample datasets?

Welcome to Bioinformatics Stackexchange @SD1024. A recently published algorithm known as MOFA (Multi-Omics Factor Analysis, paper, github) is generating a lot of interest, and is designed answer ...
Ian Sudbery's user avatar
  • 3,321

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