Data

Tools

Indexes

Applications

Experiments

Open Source Science

cite-seq-count

A tool that allows to get UMI counts from a single cell protein assay

https://github.com/hoohm/cite-seq-count

Science Score: 33.0%

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
    Links to: biorxiv.org, nature.com, zenodo.org
  • ✓
    Committers with academic emails
    1 of 10 committers (10.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.0%) to scientific vocabulary

Keywords

10x citeseq dropseq single-cell
Last synced: 6 months ago · JSON representation

Repository

A tool that allows to get UMI counts from a single cell protein assay

Basic Info
Statistics
  • Stars: 82
  • Watchers: 10
  • Forks: 44
  • Open Issues: 47
  • Releases: 3
Topics
10x citeseq dropseq single-cell
Created over 8 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License

README.md

DOI

CITE-seq-Count

A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment.

IMPORTANT NEWS

There was a major bug in version 1.3.4 of CITE-seq-Count. The results were in read counts and not in UMI counts.

This is fixed in version 1.4.0 or above. Please rerun your data as this might provide a cleaner result for your data.

Here is the website referencing the wetlab protocols needed https://cite-seq.com/

Installation

pip install CITE-seq-Count==1.4.5

The official documentation can be found here

Owner

  • Name: Patrick Roelli
  • Login: Hoohm
  • Kind: user
  • Location: Switzerland

GitHub Events

Total
  • Issues event: 3
  • Watch event: 4
  • Push event: 1
  • Pull request event: 2
  • Fork event: 2
Last Year
  • Issues event: 3
  • Watch event: 4
  • Push event: 1
  • Pull request event: 2
  • Fork event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 155
  • Total Committers: 10
  • Avg Commits per committer: 15.5
  • Development Distribution Score (DDS): 0.284
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Patrick Roelli p****i@g****m 111
Patrick Roelli r****p@b****h 29
Bill Flynn w****y@g****m 3
bbimber b****r@g****m 3
Patrick Roellip r****p@s****g 2
santiagorevale s****e@g****m 2
Gege Gui g****1@j****u 2
Arjun Arkal Rao a****o@g****m 1
Colin Davenport c****n@h****m 1
Yi Liu l****x@g****m 1
Committer Domains (Top 20 + Academic)
jhmi.edu: 1 satijalab01.nygenome.org: 1 bluewin.ch: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 113
  • Total pull requests: 7
  • Average time to close issues: 8 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 88
  • Total pull request authors: 6
  • Average comments per issue: 5.32
  • Average comments per pull request: 1.14
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: about 19 hours
  • Issue authors: 4
  • Pull request authors: 2
  • Average comments per issue: 2.2
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • bbimber (5)
  • YunZheHuang (3)
  • heathergeiger (3)
  • marianaql (3)
  • Erinke89 (3)
  • hisplan (2)
  • YingzhengXu (2)
  • naila53 (2)
  • jamesboot (2)
  • liuyang2006 (2)
  • rule-110 (2)
  • RM-SCB (2)
  • jhjlee (2)
  • sorjuela (2)
  • lldelisle (2)
Pull Request Authors
  • dtenenba (2)
  • lldelisle (2)
  • Tobiaspk (2)
  • idot (1)
  • colindaven (1)
  • Hoohm (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • pypi 120 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 15
  • Total maintainers: 1
proxy.golang.org: github.com/Hoohm/CITE-seq-Count
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 7 months ago
proxy.golang.org: github.com/hoohm/cite-seq-count
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
pypi.org: cite-seq-count

A python package to map reads from CITE-seq or hashing data for single cell experiments

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 120 Last month
Rankings
Forks count: 6.3%
Stargazers count: 8.1%
Dependent packages count: 10.0%
Average: 13.0%
Downloads: 18.6%
Dependent repos count: 21.7%
Maintainers (1)
hoohm
Last synced: 6 months ago

Dependencies

setup.py pypi
  • multiprocess >=0.70.6.1
  • pandas >=0.23.4
  • pybktree ==1.1
  • pytest ==4.1.0
  • pytest-dependency ==0.4.0
  • python-levenshtein >=0.12.0
  • scipy >=1.1.0
  • umi_tools ==1.0.0