nanostringr

NanoString QC, normalization, batch effect correction

https://github.com/talhouklab/nanostringr

Science Score: 59.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 1 DOI reference(s) in README
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Academic publication links
Links to: plos.org
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Committers with academic emails
1 of 3 committers (33.3%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.0%) to scientific vocabulary

Last synced: 6 months ago · JSON representation

Repository

NanoString QC, normalization, batch effect correction

Basic Info

Host: GitHub
Owner: TalhoukLab
License: other
Language: R
Default Branch: master
Homepage: http://talhouklab.github.io/nanostringr/
Size: 17.5 MB

Statistics

Stars: 5
Watchers: 3
Forks: 3
Open Issues: 1
Releases: 13

Created about 10 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog License

README.md

nanostringr

Overview

An R Package for quality assurance checking, normalization and batch effects adjustments of NanoString data suitable for single sample processing. This is the companion R package for the paper "Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction", published in PLOS ONE.

Installation

You can install nanostringr from CRAN with:

r install.packages("nanostringr")

Or get the latest development version from GitHub:

``` r

install.packages("devtools")

devtools::install_github("TalhoukLab/nanostringr") ```

Usage

To see the full list of exported functions:

r library(nanostringr) ls("package:nanostringr")

A quick overview of the key functions:

NanoStringQC: Computes quality assurance metrics.
HKnorm: Performs log (base 2) transformation and normalization to Housekeeping Genes
refMethod: Performs batch effect correction using the reference-based strategy
parse_counts: Read RCC files and extract raw counts data
parse_attributes: Read RCC files and extract expression annotation data

Please see citation("nanostringr") for information on how to cite the PLOS ONE paper when using this package in publications.

Owner

Name: Talhouk Lab
Login: TalhoukLab
Kind: organization

Repositories: 4
Profile: https://github.com/TalhoukLab

GitHub Events

Total

Create event: 2
Release event: 2
Issues event: 3
Issue comment event: 1
Push event: 12

Last Year

Create event: 2
Release event: 2
Issues event: 3
Issue comment event: 1
Push event: 12

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 302
Total Committers: 3
Avg Commits per committer: 100.667
Development Distribution Score (DDS): 0.159

Top Committers

Name	Email	Commits
Derek Chiu	d**u@b**a	254
Aline Talhouk	a**k@b**a	42
Derek Chiu	d**u@s**a	6

Committer Domains (Top 20 + Academic)

bccrc.ca: 2 stat.ubc.ca: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 17
Total pull requests: 7
Average time to close issues: about 2 months
Average time to close pull requests: about 10 hours
Total issue authors: 4
Total pull request authors: 1
Average comments per issue: 0.65
Average comments per pull request: 0.0
Merged pull requests: 7
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 0
Average time to close issues: 24 days
Average time to close pull requests: N/A
Issue authors: 2
Pull request authors: 0
Average comments per issue: 0.5
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

dchiu911 (12)
AlineTalhouk (3)
drkgil (1)
htseng-pstx (1)

Pull Request Authors

dchiu911 (7)

Top Labels

Issue Labels

bug (1) question (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 561 last-month
Total docker downloads: 21,613

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 13
Total maintainers: 1

cran.r-project.org: nanostringr

Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data

Homepage: https://github.com/TalhoukLab/nanostringr/
Documentation: http://cran.r-project.org/web/packages/nanostringr/nanostringr.pdf
License: MIT + file LICENSE
Latest release: 0.6.1
published 10 months ago

Versions: 13
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 561 Last month
Docker Downloads: 21,613

Rankings

Forks count: 17.8%

Stargazers count: 22.5%

Average: 27.9%

Dependent packages count: 29.8%

Downloads: 34.0%

Dependent repos count: 35.5%

Maintainers (1)

dchiu@bccrc.ca

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
assertthat * imports
ccaPP * imports
dplyr * imports
purrr * imports
rlang * imports
tidyr * imports
covr * suggests
knitr * suggests
magrittr * suggests
rmarkdown * suggests
testthat * suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action v4.4.1 composite
actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite