Questions tagged [multi-omics]
The multi-omics tag has no usage guidance.
13 questions
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What parameter and threshold to choose to get significant pathways from MetaboAnlyst pathway analysis results?
MetaboAnalyst pathway analysis results give a total of 4 different p-values viz, raw p-value, -log10 pvalue, Holm-Bonferroni adjusted p-value and the FDR value. And an impact score.
Which value should ...
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Handling duplicates in untargeted lipidomics
I have a MS-lipidomics dataset - from human samples split into a treatment group (n = 2) and control (n = 2) - which contains several detected targets that matched to the same lipid. I don't have ...
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How to calculate cell type percentage in every sample
I have a Seurat object (metadata) with the single R samples consisting of cell types and sample types columns. I am trying to make a table that has a sample and percentage of cell types for each ...
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Methylation data: beta values are normally distributed
I am trying to incorporate Methylation data (Illumina 450K) into my pipeline. I was provided with two versions of the same data: one (dataset $a$) normalized with ComBat and the other (dataset $b$) ...
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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 ...
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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 (...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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