Questions tagged [multi-omics]

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1answer
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Analyzing proteins based on sequence similarity

Using NCBI Gene database, I retrieved list of 7015 protein which are implicated in autism pathogenesis. This list includes tax-ID, organism name, symbol, aliases, map location, chromosome, genomic ...
0
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2answers
30 views

Software for microbial profiling from 16S rRNA gene sequence

I have hundreds of GBs metagenomic 16S rRNA gene sequence data. I want to do microbiome composition profiling (with relative abundance) from the data. Also after that, I will do functional profiling (...
1
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0answers
44 views

Detect differentially expressing cells

after comments on my original post, I will ask my question again here I have data (RNA expression values, obtained with multi-channel in situ hybridization) collected from 1mio human cells. For each ...
1
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0answers
97 views

Should I use log2-CPM values (voom-limma) as input for my model?

We have created a model to integrate several OMICs data, but we realized that the maximum TPM values of RNA-Seq data were so big that had unexpected effects on our results. We hypothesized that this ...
0
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2answers
74 views

Proteomics data Vs Transcriptomics data?

I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...
3
votes
1answer
867 views

Integrative analysis of omics studies using machine learning

I would like to use public omics datasets (ChIP-seq, RNA-seq, and ATAC-seq) from different studies to do an integrative analysis as follow: Normalise samples, within each type of omics, from ...
2
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2answers
44 views

How to combine multiple kernels of large sample datasets?

I have multiple large sample datasets in matrix format (each has 15000 rows and 5-50 columns) corresponding to different experiments. Each matrix contains the same number of samples(rows) but the ...
7
votes
4answers
200 views

Given a transcription factor, what genes does it regulate?

I have a list of transcription factors and I am interested in finding out which which genes might be transcribed as a result of the formation of transcription factor complexes with that transcription ...
5
votes
3answers
629 views

Is there any publicly available multi-omics dataset?

I am searching for a multi-omics dataset which may include genomics, transcriptomics and proteomics (eg. snyderome). I need such a dataset for an introductory data-exploration purpose. So it can be ...