SeqCode Web Tools

General description

The SeqCode website offers multiple applications for the analysis of genomic data. The services are basically divided into: (i) SeqCode tools for the generation of graphical results from large-scale sequencing samples (NGS tools), and (ii) general-purpose functions (Data Sets, Gene Sets and List Ops) for the analysis of lists of genes and other elements that are not part of the command line core distribution.

Please, check the following links for further information on our set of web functions:

  • Tutorials with practical examples preloaded and ready to be executed:
    [TUTORIALS]

  • Glossary of parameters and file formats of each web service:
    [FUNCTIONS OPTIONS]

Users can provide their own data file to run the following list of services with no restrictions:

  • Calculate the distribution of human/mouse genome features from a set of ChIP-seq peaks
  • Match ChIP-seq peaks to genes based in human/mouse RefSeq transcript annotations
  • Compare two sets of peaks or genomic regions to determine the degree of overlap
  • Generate boxplots with multiple graphical options to customize the final result
  • Perform PCA analysis, scatter-plots and heat-maps of genes based on expression or signal values
  • Produce Venn diagrams for multiple sets of elements and UpSet charts
  • Basic operations on lists of elements such as join, filter and fold-change analysis

The rest of functions are offered for a preselected list of ChIP-seq experiments:

  • Generate profiles of ChIPseq/ATACseq/RNAseq samples for genome browser visualizations
  • Produce high-quality aggregated plots centered around TSS, TES, TSS-TES and peak centers
  • Produce heat maps of ChIP-seq signal intensities around TSS, TES, TSS-TES and peak centers
  • Calculate the count of reads of one sequencing experiment on a set of regions


The SeqCode full distribution of commands from GitHub can be locally run with no file size restrictions: