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seqcluster

small RNA analysis from NGS data

https://github.com/lpantano/seqcluster

Science Score: 49.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.2%) to scientific vocabulary

Keywords

mirna report sequencing smallrna trna

Keywords from Contributors

nextflow nf-core differential-expression rna-seq bioinformatics closember bioconductor qc small-rna smrna-seq
Last synced: 6 months ago · JSON representation

Repository

small RNA analysis from NGS data

Basic Info
Statistics
  • Stars: 37
  • Watchers: 2
  • Forks: 17
  • Open Issues: 5
  • Releases: 9
Topics
mirna report sequencing smallrna trna
Created over 11 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.rst 

seqcluster
----------

Ask questions in the repo's Gitter: Join the chat at:

.. image:: https://badges.gitter.im/Join%20Chat.svg
    :target: https://gitter.im/lpantano/seqcluster

small RNA analysis from NGS data

.. image:: https://travis-ci.org/lpantano/seqcluster.png?branch=master
   :target: https://travis-ci.org/lpantano/seqcluster

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

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

.. image:: https://anaconda.org/bioconda/seqcluster/badges/downloads.svg
   :target: https://anaconda.org/bioconda/seqcluster

.. image:: https://img.shields.io/pypi/l/seqcluster.svg
   :target: https://github.com/lpantano/seqcluster/blob/master/LICENSE

.. image:: http://www.repostatus.org/badges/latest/active.svg
   :alt: Project Status: Active - The project has reached a stable, usable state and is being actively developed.
   :target: http://www.repostatus.org/#active

.. image:: https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtv632-lightgrey.svg?style=flat-square
   :target: https://doi.org/10.1093/bioinformatics/btv632

Cite
---------

**Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis**. Pantano L, Friedländer MR, Escaramís G, Lizano E, Pallarès-Albanell J, Ferrer I, Estivill X, Martí E.
Bioinformatics. 2015 Nov 2. pii: btv632. [Epub ahead of print]
PMID: `26530722 `_

**A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.**
Pantano L1, Estivill X, Martí E. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.
PMID: `21976421 `_

Quick start links
---------

See installation at http://seqcluster.readthedocs.org/installation.html

Moreover `bcbio-nextgen`_ provides
a python framework to run a whole pipeline for small RNA (miRNA + tRNA + piRNA + others).

.. _bcbio-nextgen: https://bcbio-nextgen.readthedocs.org/en/latest/

An example of how to run with bcbio is here: http://seqcluster.readthedocs.org/example_pipeline.html#mirqc-data

In case you want to use seqcluster alone, a complete tutorial is here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences

Report
---------

Seqcluster creates html report that looks like `this`_. That is a table of all cluster detected, and you
can go into each of them and get a complete `description`_ with profile expression figures, annotation details and
sequences counts for each sample. An interactive report is as well available to explore the expression profile,
position on the genome and secondary structure. Learn more http://seqcluster.readthedocs.org/more_outputs.html#report.

.. _this: https://rawgit.com/lpantano/seqcluster/master/data/examples_report/html/index.html
.. _description: https://rawgit.com/lpantano/seqcluster/master/data/examples_report/html/1/maps.html

Contributors
------------

* `Lorena Pantano  `_ (Bioinformatic Core, Harvard Chan School, Boston, USA)
* `Judith Flo Gaya `_ (School of Engineer and Aplied Science- Harvard University, Boston, USA)
* `Eulalia Marti Puig `_ (Genomics and Disease, Center of Genomic Regulation, Barcelona, Spain)
* Francisco Pantano Rubino: Architect
* `Steffen Möller `_ (University of Rostock)

.. image:: https://d2weczhvl823v0.cloudfront.net/lpantano/seqcluster/trend.png
   :alt: Bitdeli badge
   :target: https://bitdeli.com/free

Owner

  • Name: Lorena Pantano
  • Login: lpantano
  • Kind: user
  • Location: Boston

PhD in miRNA analysis in mental disease @ CRG, Barcelona, Spain. Experience in NGS data analysis. Love python, R, and data integration. twitter:@lopantano

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 849
  • Total Committers: 8
  • Avg Commits per committer: 106.125
  • Development Distribution Score (DDS): 0.049
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Lorena l****o@g****m 807
Lorena Pantano l****a@v****e 25
Steffen Möller m****r@d****g 12
Karolis Kalantojus k****s@v****u 1
Alex Bartlett a****t@n****m 1
chapmanb c****b@5****m 1
Lorena Pantano l****o@a****m 1
Bitdeli Chef c****f@b****m 1
Committer Domains (Top 20 + Academic)
bitdeli.com: 1 axcellahealth.com: 1 50mail.com: 1 nextrna.com: 1 versada.eu: 1 debian.org: 1 vpantano.name: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 41
  • Total pull requests: 18
  • Average time to close issues: almost 2 years
  • Average time to close pull requests: 11 days
  • Total issue authors: 23
  • Total pull request authors: 8
  • Average comments per issue: 5.41
  • Average comments per pull request: 1.72
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 14 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 4.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • lpantano (11)
  • smoe (5)
  • hmkim (3)
  • AlexandraBomane (3)
  • sung (1)
  • jxshi (1)
  • kisun (1)
  • ramaniak (1)
  • ahsen1402 (1)
  • SarahLuca (1)
  • YangZituo (1)
  • Alarabi1980 (1)
  • lurebgi (1)
  • gnvalbuena (1)
  • charles-xue (1)
Pull Request Authors
  • smoe (7)
  • lpantano (4)
  • chapmanb (2)
  • emollier (2)
  • kkarolis (1)
  • gitter-badger (1)
  • abartlett004 (1)
  • bitdeli-chef (1)
Top Labels
Issue Labels
enhancement (7) bug (1) question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 11 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 39
  • Total maintainers: 1
pypi.org: seqcluster

Small RNA-seq pipeline

  • Versions: 39
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 11 Last month
  • Docker Downloads: 0
Rankings
Docker downloads count: 1.2%
Dependent repos count: 9.0%
Forks count: 9.1%
Dependent packages count: 10.0%
Average: 10.5%
Stargazers count: 10.8%
Downloads: 22.8%
Maintainers (1)
lpantano
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • biopython *
  • colorlog *
  • mirtop *
  • nose >=1.3.0
  • numpy *
  • pandas >=0.14.1
  • progressbar2 *
  • pybedtools >=0.6.8
  • pysam >=0.8.2.1
  • pytz *
  • pyyaml *
  • scipy >=0.15.1
setup.py pypi
  • x.strip *
Dockerfile docker
  • ubuntu latest build