What are the data formats accepted by OmicsAnalyst?

OmicsAnalyst
1

OmicsAnalyst accepts two or more feature abundance tables generated from common omics technologies such as transcriptomics, proteomics, metabolomics, microbiome, and miRNA data.

Features must be in rows and samples in columns (example below). Files must either be in .txt, .csv, or their compressed format (.zip).

Example Abundance File (containing metadata)

   #NAME               sample10    sample105   sample11    sample113
   #CLASS:Condition    Classical   Classical   Classical   Classical
   FSTL1               0.04085     1.09922     -0.45374    0.03402
   MMP2                1.76569     -0.50303    0.41764     1.25827
   BBOX1               0.9542      1.21379     0.95196     0.60273
   GCSH                0.59383     0.66385     -0.00448    0.47665
   EDN1                0.8455      -0.26195    -0.34848    0.08309
   CXCR4               0.1691      0.04824     0.47361     -0.55183
   SALL1               0.45267     0.97534     0.35652     1.32005
   MMP7                -1.47079    -1.29109    -1.40518    -1.08673
   ......

Example Abundance File (metadata in a separate file below)

   #NAME               sample10    sample105   sample11    sample113
   FSTL1               0.04085     1.09922     -0.45374    0.03402
   MMP2                1.76569     -0.50303    0.41764     1.25827
   BBOX1               0.9542      1.21379     0.95196     0.60273
   GCSH                0.59383     0.66385     -0.00448    0.47665
   EDN1                0.8455      -0.26195    -0.34848    0.08309
   CXCR4               0.1691      0.04824     0.47361     -0.55183
   SALL1               0.45267     0.97534     0.35652     1.32005
   MMP7                -1.47079    -1.29109    -1.40518    -1.08673
   ......

A metadata file (upload together with the above feature abundance file)

   #NAME          Condition   Gender
   sample10       Classical    M
   sample105      Classical    M
   sample11       Classical    F
   sample113      Classical    M
   ......

Notes about formatting your data files:

  • Sample and feature names must be unique and consist of a combination of common English letters, underscores and numbers for naming purpose. Latin/Greek letters are not supported.
  • Sample names must be consistent across all files (i.e. omics abundance tables and metadata file).
  • Data values should contain only numeric values. Empty cells or cells with NA values are considered missing values.
  • If you include metadata in the feature abundance file, metadata or group label should directly below sample names indicated by “#CLASS”. You can indicated multiple factors. For instance, the above TCGA example data sets contains two factors indicated by “#CLASS:Condition”, “#CLASS:Hours”, respectively.