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Integrative analysis of high-thoughput sequencing data

Project description

https://travis-ci.org/daler/metaseq.svg?branch=master

Briefly, the goal of metaseq is to tie together lots of existing software into a framework for exploring genomic data. It focuses on flexibility and interactive exploration and plotting of disparate genomic data sets.

The main documentation for metaseq can be found at http://packages.python.org/metaseq/.

Example 1: Average ChIP-seq signal over promoters

Example 1 walks you through the creation of the following heatmap and line-plot figure:

demo.png

Top: Heatmap of ATF3 ChIP-seq signal over transcription start sites (TSS) on chr17 in human K562 cells. Middle: average ChIP enrichment over all TSSs +/- 1kb, with 95% CI band. Bottom: Integration with ATF3 knockdown RNA-seq results, showing differential enrichment over transcripts that went up, down, or were unchanged upon ATF3 knockdown.

Example 2: Differential expression scatterplots

Example 2 walks you through the creation of the following scatterplot and marginal histogram figure:

expression-demo.png

Control vs knockdown expression (log2(FPKM + 1)) for an ATF3 knockdown experiment. Each point represents one transcript on chromosome 17. Marginal distributions are shown on top and side. 1:1 line shown as a dotted line. Up- and downregulated genes determined by a simple 2-fold cutoff.

Other features

In addition, metaseq offers:

  • A format-agnostic API for accessing “genomic signal” that allows you to work with BAM, BED, VCF, GTF, GFF, bigBed, and bigWig using the same API.
  • Parallel data access from the file formats mentioned above
  • “Mini-browsers”, zoomable and pannable Python-only figures that show genomic signal and gene models and are spawned by clicking on features of interest
  • A wrapper around pandas.DataFrames to simplify the manipulation and plotting of tabular results data that contain gene information (like DESeq results tables)
  • Integrates data keyed by genomic interval (think BAM or BED files) with data keyed by gene ID (e.g., Cufflinks or DESeq results tables)

Check out the full documentation for more.

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Filename, size & hash SHA256 hash help File type Python version Upload date
metaseq-0.5.3.tar.gz (1.3 MB) Copy SHA256 hash SHA256 Source None Jun 9, 2014

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