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AneuFinder

Find CNVs in single cell sequencing data.

https://github.com/ataudt/aneufinder

Science Score: 10.0%

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
  • ✓
    Committers with academic emails
    1 of 16 committers (6.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.4%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene proteomics u24ca289073 core-package bioinformatics bioconductor cell-free-dna copy-number loh
Last synced: 11 months ago · JSON representation

Repository

Find CNVs in single cell sequencing data.

Basic Info
  • Host: GitHub
  • Owner: ataudt
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 35.9 MB
Statistics
  • Stars: 18
  • Watchers: 3
  • Forks: 19
  • Open Issues: 6
  • Releases: 2
Created about 12 years ago · Last pushed over 3 years ago
Metadata Files
Readme

README.md

bioc bioc

AneuFinder

Copy-number detection in single-cell whole genome sequencing (scWGS) and Strand-seq data using a Hidden Markov Model or binary bisection method. The package implements copy-number detection, estimation of breakpoints with confidence intervals, hotspot detection, commonly used plotting functions, export to BED format for upload to genome browsers, and measures for assessment of karyotype heterogeneity and quality metrics.

Installation

Stable release version from Bioconductor

To install the current stable version from Bioconductor, please visit http://bioconductor.org/packages/AneuFinder/ and follow the provided instructions.

Development version from Github

To install the development version from Github, follow the steps given below. The installation has only been tested on Ubuntu so far, if you need to install on Windows or Mac additional steps might be necessary (e.g. installation of Rtools from https://cran.r-project.org/bin/windows/Rtools/)

  1. Install a recent version of R (>3.3) from https://www.r-project.org/
  2. Optional: For ease of use, install Rstudio from https://www.rstudio.com/
  3. Open R and install all dependencies. Please ensure that you have writing permissions to install packages. Execute the following lines one by one:

install.packages("devtools")
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("GenomicRanges")
BiocManager::install("GenomicAlignments")
library(devtools)
installgithub("ataudt/aneufinderData")
installgithub("ataudt/aneufinder")
#### Or alternatively if the above line doesn't work:
installgit("git://github.com/ataudt/aneufinderData.git", branch = "master")
installgit("git://github.com/ataudt/aneufinder.git", branch = "master")

How to use AneuFinder

Please refer to the vignette on Bioconductor for tutorials on how to use AneuFinder.

Report Errors

If you encounter errors of any kind, please file an issue here. I will try to react within a week.

Owner

  • Name: Aaron
  • Login: ataudt
  • Kind: user

Coding enthusiast, chief technology officer, runner, foody, ...

GitHub Events

Total
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Fork event: 2
Last Year
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Fork event: 2

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 411
  • Total Committers: 16
  • Avg Commits per committer: 25.688
  • Development Distribution Score (DDS): 0.185
Past Year
  • Commits: 5
  • Committers: 2
  • Avg Commits per committer: 2.5
  • Development Distribution Score (DDS): 0.4
Top Committers
Name Email Commits
chakalakka a****t@u****l 335
Aaron Taudt a****t@g****m 24
Nitesh Turaga n****a@g****m 14
chakalakka a****t@g****t 10
Hervé Pagès h****s@f****g 7
Dan Tenenbaum d****a@f****g 4
Herve Pages h****s@f****g 4
daewooo d****o@g****m 2
vobencha v****a@g****m 2
vobencha v****n@r****g 2
J Wokaty j****y@s****u 2
daewooo d****y@g****m 1
Martin Morgan m****n@f****g 1
Kayla-Morrell k****l@r****g 1
LiNk-NY m****9@g****m 1
Hervé Pagès h****b@g****m 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 3 roswellpark.org: 2 sph.cuny.edu: 1 fredhutch.org: 1 gmx.net: 1 umcg.nl: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 12
  • Total pull requests: 1
  • Average time to close issues: about 1 year
  • Average time to close pull requests: N/A
  • Total issue authors: 11
  • Total pull request authors: 1
  • Average comments per issue: 1.08
  • Average comments per pull request: 4.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mschubert (2)
  • roelj (1)
  • shouguog (1)
  • PingpingQu-bio (1)
  • leon8889 (1)
  • ghost (1)
  • proukakis (1)
  • al3xmlt030 (1)
  • Yannick-Kok (1)
  • william-c-chen (1)
  • clauswilke (1)
  • EularTang (1)
Pull Request Authors
  • MaiseB (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • bioconductor 35,858 total
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 7
  • Total maintainers: 1
proxy.golang.org: github.com/ataudt/aneufinder
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 12 months ago
bioconductor.org: AneuFinder

Analysis of Copy Number Variation in Single-Cell-Sequencing Data

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 35,858 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 16.1%
Downloads: 48.4%
Maintainers (1)
aaron.taudt@gmail.com
Last synced: 12 months ago

Dependencies

DESCRIPTION cran
  • AneuFinderData * depends
  • GenomicRanges * depends
  • R >= 3.5 depends
  • cowplot * depends
  • ggplot2 * depends
  • BiocGenerics >= 0.31.6 imports
  • Biostrings * imports
  • DNAcopy * imports
  • GenomeInfoDb * imports
  • GenomicAlignments * imports
  • IRanges * imports
  • ReorderCluster * imports
  • Rsamtools * imports
  • S4Vectors * imports
  • bamsignals * imports
  • doParallel * imports
  • ecp * imports
  • foreach * imports
  • ggdendro * imports
  • ggrepel * imports
  • grDevices * imports
  • graphics * imports
  • mclust * imports
  • methods * imports
  • reshape2 * imports
  • stats * imports
  • utils * imports
  • BSgenome.Hsapiens.UCSC.hg19 * suggests
  • BSgenome.Mmusculus.UCSC.mm10 * suggests
  • BiocStyle * suggests
  • knitr * suggests
  • testthat * suggests