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BioT2Ex
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biologo

Introduction

Biologists and clinicians are addicted to Excel. However, most tools and software in the community prefer to output txt- or csv-formatted results. There is a gap between the well-annotated excel file and raw analysis results exported from bio-software. To address this issue, we launched the BioT2Ex project that provides a package or toolkit to conveniently convert the tabular txt file into a well-anotated Excel file. We believe this project could facilitate the downstream data interpretation of high-throughput genomic sequencing analysis.

What can this project do?

1.Convert the output to a file in XLSX format

The output files of many analysis tools are not in XLSX format and are not easily understood. BioT2Ex can convert most analysis tool output files to XLSX format for enhanced visualization and understanding.

2.Add annotations to analysis results

  • Add the “up-down” comment column
  • Add ENTREZID
  • Add GO term and GeneBank link of each gene
  • Add gradient color to the logFC column to indicate the expression level
  • Add statistical functions for some specific variables
  • Add gene description
  • Add comment information for the header
  • Make the numbers appear in the correct format

Features

  • Easy to install

    Python:

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    pip install BioT2Ex

    R:

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    if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")

    BiocManager::install("BioT2Ex")

  • Quick usage

    Please refer to Docunments for detailed usage on the Docs page.

    Python:

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    #macs
    Python BioT2Ex -m macs [path of the inputfile]
    #MutSigCV
    Python BioT2Ex -m mutsigcv [path of the inputfile]
    #rsem
    Python BioT2Ex -m rsem [path of the inputfile]

    R:

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    #edgeR
    render_edgeR(input,orgDB,taxid,n,filename,showInExcel)
    #DESeq2
    render_DESeq2(input,orgDB,taxid,filename,n,showInExcel)
    #limma
    render_limma(input,orgDB,taxid,filename,n,showInExcel)
    #NOIseq
    render_NOISeq(input,orgDB,taxid,filename,n,showInExcel)
    #clusterProfiler
    render_clusterP_GO(input,filename,showInExcel)
    render_clusterP_KEGG(input,filename,showInExcel)
    #ChIPseeker
    render_ChIPseeker(input,orgDB,taxid,filename,op)
    #DiffBind
    render_DiffBind(input,n,filename="",sheetname="",taxid,showInExcel)

  • Customize software-specific results conversion to excel

  • Highlight and annotate items in excels

  • Build publishable tables

  • Pipe to downstream functional analysis software

  • Add relevant annotations

Output effect

edgeR:

edgeR

MACS:

macs

Support softwares

RNAseq software | ChIPseq software | Wes data software

See the detailed tool list:Supported-tools page.