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bcbio-gff

Incubator for useful bioinformatics code, primarily in Python and R

https://github.com/chapmanb/bcbb

Science Score: 23.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    8 of 36 committers (22.2%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.3%) to scientific vocabulary

Keywords from Contributors

bioinformatics ngs pypi vizualisation seqera reporting quality-control multiqc bioconda usegalaxy
Last synced: 10 months ago · JSON representation

Repository

Incubator for useful bioinformatics code, primarily in Python and R

Basic Info
Statistics
  • Stars: 630
  • Watchers: 57
  • Forks: 243
  • Open Issues: 19
  • Releases: 0
Created over 17 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

Collection of useful code related to biological analysis. Much of this is discussed with examples at Blue collar bioinformatics.

All code, images and documents in this repository are freely available for all uses. Code is available under the MIT license and images, documentations and talks under the Creative Commons No Rights Reserved (CC0) license.

Some projects which may be especially interesting:

  • CloudBioLinux -- An automated environment to install useful biological software and libraries. This is used to bootstrap blank machines, such as those you'd find on Cloud providers like Amazon, to ready to go analysis workstations. See the CloudBioLinux effort for more details. This project moved to its own repository at https://github.com/chapmanb/cloudbiolinux.
  • gff -- A GFF parsing library in Python, aimed for inclusion into Biopython.
  • nextgen -- A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. This project has moved into its own repository: https://github.com/chapmanb/bcbio-nextgen
  • distblast -- A distributed BLAST analysis running for identifying best hits in a wide variety of organisms for downstream phylogenetic analyses. The code is generalized to run on local multi-processor and distributed Hadoop clusters.

Owner

  • Name: Brad Chapman
  • Login: chapmanb
  • Kind: user
  • Location: Boston, MA
  • Company: Ginkgo Bioworks

Biologist and programmer

GitHub Events

Total
  • Watch event: 16
  • Issue comment event: 1
  • Push event: 1
  • Pull request event: 4
  • Fork event: 2
Last Year
  • Watch event: 16
  • Issue comment event: 1
  • Push event: 1
  • Pull request event: 4
  • Fork event: 2

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 1,321
  • Total Committers: 36
  • Avg Commits per committer: 36.694
  • Development Distribution Score (DDS): 0.152
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
chapmanb c****b@5****m 1,120
Roman Valls Guimera r****a@s****e 52
roryk r****r@g****m 34
Brad Chapman c****b@k****) 22
Roman Valls Guimerà b****m@n****g 21
Roman Valls Guimerà r****g@k****e 10
Brad Chapman c****n@m****u 7
Valentine Svensson v****e@n****e 7
peterjc p****k@g****m 6
Keith Hughitt k****t@g****m 4
Brad c****n@g****u 3
Roman Valls r****g@s****e 3
rvalls r****s@b****) 3
Matt Spinelli m****e@g****m 3
Chris Anderson j****s@g****t 2
Yi Hsiao h****4@g****m 2
John Morrissey j****m@h****t 2
Tim Burke t****e@g****m 2
Cory McLean c****m@g****m 1
Dan Fornika d****a@g****m 1
DavyCats d****c@g****m 1
Hugh Zhu h****9@g****m 1
John Didion g****b@d****t 1
Kwok Lab l****g@u****u 1
Mitch Skinner g****t@a****s 1
Nomi Harris n****s 1
Winston Hide w****e@h****u 1
Oliver Hofmann o****n@h****u 1
Henning Redestig h****g@b****m 1
Peter Haverty p****y@g****m 1
and 6 more...
Committer Domains (Top 20 + Academic)
hsph.harvard.edu: 3 50mail.com: 1 scilifelab.se: 1 kunkel.(none): 1 nopcode.org: 1 kth.se: 1 mothra.mgh.harvard.edu: 1 nxn.se: 1 galaga.mgh.harvard.edu: 1 sbc.su.se: 1 biobit.(none): 1 grabb.it: 1 horde.net: 1 google.com: 1 didion.net: 1 ucsf.edu: 1 arctur.us: 1 bayer.com: 1 ginkgobioworks.com: 1 lumc.nl: 1 inria.fr: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 50
  • Total pull requests: 60
  • Average time to close issues: 4 months
  • Average time to close pull requests: 14 days
  • Total issue authors: 37
  • Total pull request authors: 28
  • Average comments per issue: 2.34
  • Average comments per pull request: 1.18
  • Merged pull requests: 40
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: about 15 hours
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.25
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • victorlin (4)
  • hexylena (3)
  • khughitt (3)
  • inti (3)
  • sjackman (3)
  • bobbyo (2)
  • zeynepkurtw (2)
  • mikdur (1)
  • Rhinogradentia (1)
  • mercutio22 (1)
  • vineeth-s (1)
  • NtBaru (1)
  • camilo-monge (1)
  • tiagoantao (1)
  • corneliusroemer (1)
Pull Request Authors
  • brainstorm (18)
  • roryk (11)
  • emollier (4)
  • mspinelli (2)
  • jwm (2)
  • hsiaoyi0504 (2)
  • phaverty-ginkgo (2)
  • timgates42 (2)
  • fubar2 (2)
  • TheOneHyer (1)
  • victorlin (1)
  • hredestig (1)
  • kwoklab-user (1)
  • sergiuser1 (1)
  • tipabu (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 17,472 last-month
  • Total docker downloads: 534
  • Total dependent packages: 20
  • Total dependent repositories: 105
  • Total versions: 15
  • Total maintainers: 1
pypi.org: bcbio-gff

Read and write Generic Feature Format (GFF) with Biopython integration.

  • Versions: 15
  • Dependent Packages: 20
  • Dependent Repositories: 105
  • Downloads: 17,472 Last month
  • Docker Downloads: 534
Rankings
Dependent packages count: 0.6%
Docker downloads count: 1.0%
Dependent repos count: 1.5%
Average: 2.1%
Stargazers count: 2.6%
Forks count: 3.4%
Downloads: 3.7%
Maintainers (1)
chapmanb
Last synced: 11 months ago

Dependencies

biostar/bed-hadoop/project.clj clojars
  • cascalog 1.8.0-SNAPSHOT
  • org.clojure/clojure 1.2.1
biostar/biostar.ngschallenge/project.clj clojars
  • bcbio.variation 0.0.1-SNAPSHOT
  • org.clojure/clojure 1.3.0
biostar/findorf/project.clj clojars
  • org.biojava/biojava3-core 3.0.1
  • org.clojure/clojure 1.2.0
  • org.clojure/clojure-contrib 1.2.0
distblast/setup.py pypi
  • PyYAML *
  • biopython *
gff/setup.py pypi
  • six *