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metaseq

Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data

https://github.com/daler/metaseq

Science Score: 20.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.6%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data

Basic Info
Statistics
  • Stars: 87
  • Watchers: 21
  • Forks: 36
  • Open Issues: 15
  • Releases: 0
Created over 14 years ago · Last pushed almost 6 years ago
Metadata Files
Readme License

README.rst 

Metaseq
=======
.. image:: https://travis-ci.org/daler/metaseq.png?branch=master
    :target: https://travis-ci.org/daler/metaseq

.. image:: https://badge.fury.io/py/metaseq.svg
    :target: http://badge.fury.io/py/metaseq

.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
    :target: http://bioconda.github.io

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 https://daler.github.io/metaseq.

If you use `metaseq` in your work, please cite the following publication:

    Dale, R. K., Matzat, L. H. & Lei, E. P. metaseq: a Python package for
    integrative genome-wide analysis reveals relationships between chromatin
    insulators and associated nuclear mRNA. Nucleic Acids Res. 42, 9158–9170
    (2014). http://www.ncbi.nlm.nih.gov/pubmed/25063299


Example 1: Average ChIP-seq signal over promoters
-------------------------------------------------

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

.. 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:


.. 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.

Owner

  • Name: Ryan Dale
  • Login: daler
  • Kind: user
  • Location: Bethesda, MD
  • Company: National Institutes of Health (NIH), National Institute of Child Health and Human Development (NICHD)

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 470
  • Total Committers: 3
  • Avg Commits per committer: 156.667
  • Development Distribution Score (DDS): 0.011
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
daler d****r@n****v 465
Olga Botvinnik o****k@g****m 4
Alexis GRIMALDI a****i@g****m 1
Committer Domains (Top 20 + Academic)
niddk.nih.gov: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 37
  • Total pull requests: 6
  • Average time to close issues: 29 days
  • Average time to close pull requests: about 7 hours
  • Total issue authors: 25
  • Total pull request authors: 4
  • Average comments per issue: 3.14
  • Average comments per pull request: 0.33
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kellermac (9)
  • ghost (3)
  • sumanex (2)
  • daler (2)
  • imk1 (1)
  • quantumdot (1)
  • zhenyisong (1)
  • jlpulice (1)
  • Liyi56 (1)
  • i000 (1)
  • magruca (1)
  • Fiona-and-Cake (1)
  • semenko (1)
  • sqs1020 (1)
  • oxpeter (1)
Pull Request Authors
  • daler (3)
  • olgabot (1)
  • opoirion (1)
  • grmwld (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 59 last-month
  • Total docker downloads: 55
  • Total dependent packages: 0
  • Total dependent repositories: 8
  • Total versions: 14
  • Total maintainers: 1
pypi.org: metaseq

Integrative analysis of high-thoughput sequencing data

  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 8
  • Downloads: 59 Last month
  • Docker Downloads: 55
Rankings
Docker downloads count: 3.1%
Dependent repos count: 5.2%
Forks count: 6.7%
Stargazers count: 7.6%
Average: 9.4%
Dependent packages count: 10.0%
Downloads: 23.8%
Maintainers (1)
daler
Last synced: 12 months ago

Dependencies

bioconda-requirements.txt pypi
  • bedtools *
  • htslib *
  • samtools *
  • ucsc-bedgraphtobigwig *
  • ucsc-bedtobigbed *
  • ucsc-bigwigsummary *
  • ucsc-bigwigtobedgraph *
docs-requirements.txt pypi
  • jupyter *
  • nbconvert *
  • numpydoc *
  • pandoc *
  • pygments *
  • sphinx *
requirements.txt pypi
  • Cython *
  • PyYAML >=3.10
  • biopython *
  • bx-python >=0.7.1
  • fisher *
  • gffutils >=0.8.2
  • matplotlib >=1.3.1
  • numpy >=1.8.0
  • pandas >=0.13.1
  • pybedtools >=0.6.6
  • pysam >=0.7
  • scikit-learn *
  • scipy >=0.10.1