twosamplemr

R package for performing 2-sample MR using IEU OpenGWAS database

https://github.com/mrcieu/twosamplemr

Science Score: 62.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
✓
Committers with academic emails
13 of 28 committers (46.4%) from academic institutions
✓
Institutional organization owner
Organization mrcieu has institutional domain (www.bristol.ac.uk)
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (3.5%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

R package for performing 2-sample MR using IEU OpenGWAS database

Basic Info

Host: GitHub
Owner: MRCIEU
License: other
Language: R
Default Branch: master
Homepage: http://mrcieu.github.io/TwoSampleMR/
Size: 61.4 MB

Statistics

Stars: 506
Watchers: 28
Forks: 184
Open Issues: 119
Releases: 30

Created about 10 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

README.Rmd

---
output: github_document
---



```{r, child='index.md'}
```



## Documentation

**Full documentation available here:** https://mrcieu.github.io/TwoSampleMR/

Owner

Name: MRC Integrative Epidemiology Unit
Login: MRCIEU
Kind: organization
Location: University of Bristol, UK

Website: www.bristol.ac.uk/ieu
Repositories: 63
Profile: https://github.com/MRCIEU

Citation (CITATION.cff)

cff-version: 1.2.0
message: "Please cite this software using the metadata from 'preferred-citation'."
authors:
- family-names: "Hemani"
  given-names: "Gibran"
  orcid: "https://orcid.org/0000-0003-0920-1055"
- family-names: "Haycock"
  given-names: "Philip"
  orcid: "https://orcid.org/0000-0001-5001-3350"
- family-names: "Zheng"
  given-names: "Jie"
  orcid: "https://orcid.org/0000-0002-6623-6839"
- family-names: "Gaunt"
  given-names: "Tom"
  orcid: "https://orcid.org/0000-0003-0924-3247"
- family-names: "Elsworth"
  given-names: "Ben"
  orcid: "https://orcid.org/0000-0001-7328-4233"
- family-names: "Palmer"
  given-names: "Tom"
  orcid: "https://orcid.org/0000-0003-4655-4511"
title: "TwoSampleMR R package"
type: software
version: 0.5.8
date-released: 2023-11-16
doi: "10.5281/zenodo.4636570"
url: "https://mrcieu.github.io/TwoSampleMR/index.html"
repository-code: "https://github.com/MRCIEU/TwoSampleMR"
license: MIT
preferred-citation:
  authors:
    - family-names: "Hemani"
      given-names: "Gibran"
      orcid: "https://orcid.org/0000-0003-0920-1055"
    - family-names: "Zheng"
      given-names: "Jie"
      orcid: "https://orcid.org/0000-0002-6623-6839"
    - family-names: "Elsworth"
      given-names: "Ben"
      orcid: "https://orcid.org/0000-0001-7328-4233"
    - family-names: "Wade"
      given-names: "Kaitlin"
      orcid: "https://orcid.org/0000-0003-3362-6280"
    - family-names: "Haberland"
      given-names: "Valeriia"
      orcid: "https://orcid.org/0000-0002-3874-0683"
    - family-names: "Baird"
      given-names: "Denis"
      orcid: "https://orcid.org/0000-0003-4600-6013"
    - family-names: "Laurin"
      given-names: "Charles"
      orcid: "https://orcid.org/0000-0003-2439-9004"
    - family-names: "Burgess"
      given-names: "Stephen"
      orcid: "https://orcid.org/0000-0001-5365-8760"
    - family-names: "Bowden"
      given-names: "Jack"
      orcid: "https://orcid.org/0000-0003-2628-3304"
    - family-names: "Langdon"
      given-names: "Ryan"
      orcid: "https://orcid.org/0000-0003-3543-6480"
    - family-names: "Tan"
      given-names: "Vanessa Y"
    - family-names: "Yarmolinsky"
      given-names: "James"
      orcid: "https://orcid.org/0000-0003-4371-0873"
    - family-names: "Shibab"
      given-names: "Hashem"
    - family-names: "Timpson"
      given-names: "Nicholas"
      orcid: "https://orcid.org/0000-0002-7141-9189"
    - family-names: "Evans"
      given-names: "David"
      orcid: "https://orcid.org/0000-0003-0663-4621"
    - family-names: "Relton"
      given-names: "Caroline"
      orcid: "https://orcid.org/0000-0003-2052-4840"
    - family-names: "Martin"
      given-names: "Richard"
      orcid: "https://orcid.org/0000-0002-7992-7719"
    - family-names: "Davey Smith"
      given-names: "George"
      orcid: "https://orcid.org/0000-0002-1407-8314"
    - family-names: "Gaunt"
      given-names: "Tom"
      orcid: "https://orcid.org/0000-0003-0924-3247"
    - family-names: "Haycock"
      given-names: "Philip"
      orcid: "https://orcid.org/0000-0001-5001-3350"
    - name: "The MR-Base Collaboration"
  title: "The MR-Base platform supports systematic causal inference across the human phenome"
  type: article
  journal: "eLife"
  volume: "7"
  start: "e34408"
  year: "2018"
  doi: "10.7554/eLife.34408"
  url: "https://elifesciences.org/articles/34408"
references:
  - authors: 
      - family-names: "Hemani"
        given-names: "Gibran"
        orcid: "https://orcid.org/0000-0003-0920-1055"
      - family-names: "Tilling"
        given-names: "Kate"
        orcid: "https://orcid.org/0000-0002-1010-8926"
      - family-names: "Davey Smith"
        given-names: "George"
        orcid: "https://orcid.org/0000-0002-1407-8314"
    title: "Orienting the causal relationship between imprecisely measured traits using GWAS summary data"
    type: article
    journal: "PLoS Genetics"
    year: "2017"
    volume: "13"
    number: "11"
    start: "e1007081"
    doi: "10.1371/journal.pgen.1007081"
    url: "https://doi.org/10.1371/journal.pgen.1007081"

GitHub Events

Total

Create event: 8
Commit comment event: 1
Release event: 6
Issues event: 162
Watch event: 66
Issue comment event: 145
Push event: 38
Pull request event: 44
Fork event: 10

Last Year

Create event: 8
Commit comment event: 1
Release event: 6
Issues event: 162
Watch event: 66
Issue comment event: 145
Push event: 38
Pull request event: 44
Fork event: 10

Committers

Last synced: over 2 years ago

All Time

Total Commits: 1,324
Total Committers: 28
Avg Commits per committer: 47.286
Development Distribution Score (DDS): 0.489

Past Year

Commits: 259
Committers: 2
Avg Commits per committer: 129.5
Development Distribution Score (DDS): 0.004

Top Committers

Name	Email	Commits
Tom Palmer	r**t@h**m	676
Gibran Hemani	e**r@g**m	504
Philip Haycock	p**k@b**k	54
Philip Haycock	p**6@b**k	20
PC Haycock	p**6@i**k	14
qingyuanzhao	q**o@g**m	7
Charles Laurin	c**2@b**k	6
Tom Gaunt	t****g	5
ph14916	p**6@e**k	5
Matthew Lyon	m**2@n**r	4
Matthew Lyon	m**2@n**r	4
geneinmylife	e**z@b**k	3
jinghuazhao@github.com	j**o@h**m	3
conorjudge	5****e	2
Gib Hemani	g**i@b**k	2
Conor Judge	c**e@g**m	2
Clare	3****t	2
Kaitlin Wade	k**5@b**k	1
Gibran Hemani	g**7@s**k	1
Yossi Farjoun	f**n@g**m	1
Matthew Lyon	m**n@b**k	1
ph14916	p**6@i**l	1
Mischa Lundberg	l**a@g**m	1
Gibran Hemani	g**7@v**k	1
Leland Taylor	l****r	1
Matthew Lyon	ml@e****k	1
Qingyuan Zhao	q**o@H**l	1
Matthew Lyon	ml@e****k	1

Committer Domains (Top 20 + Academic)

bristol.ac.uk: 7 eduroam-179-115.nomadic.bris.ac.uk: 1 eduroam-254-182.nomadic.bris.ac.uk: 1 vpn-user-248-053.nomadic.bris.ac.uk: 1 scmv-webapps.epi.bris.ac.uk: 1 newblue2.cm.cluster: 1 newblue4.cm.cluster: 1 eduroam-ubht-168-175.nomadic.bris.ac.uk: 1 it017413.users.bris.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 134
Total pull requests: 22
Average time to close issues: over 3 years
Average time to close pull requests: about 4 hours
Total issue authors: 110
Total pull request authors: 3
Average comments per issue: 2.34
Average comments per pull request: 0.18
Merged pull requests: 15
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 31
Pull requests: 22
Average time to close issues: 15 days
Average time to close pull requests: about 4 hours
Issue authors: 29
Pull request authors: 3
Average comments per issue: 0.94
Average comments per pull request: 0.18
Merged pull requests: 15
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

explodecomputer (8)
JonnyBaseball (5)
jonnyrose (5)
yongkang1230 (4)
tj0129edgar (3)
zjralkc (3)
a1141539455 (3)
AleRaho (2)
dongchaoanderuni (2)
ASSO-bot (2)
amaa11 (2)
M-jk22 (2)
ketzelehs (2)
phageghost (2)
jennysjaarda (2)

Pull Request Authors

remlapmot (31)
explodecomputer (3)
jinghuazhao (1)
sasaju (1)
yatest (1)
zhangbing12313 (1)
leoarrow1 (1)
ronaldo7-star (1)
zznx (1)

Top Labels

Issue Labels

bug (94) enhancement (12)

Pull Request Labels

bug (3)

Packages

Total packages: 2
Total downloads: unknown

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 58

proxy.golang.org: github.com/MRCIEU/TwoSampleMR

Documentation: https://pkg.go.dev/github.com/MRCIEU/TwoSampleMR#section-documentation
License: other
Latest release: v0.6.22
published 6 months ago

Versions: 29
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.5%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 6 months ago

proxy.golang.org: github.com/mrcieu/twosamplemr

Documentation: https://pkg.go.dev/github.com/mrcieu/twosamplemr#section-documentation
License: other
Latest release: v0.6.22
published 6 months ago

Versions: 29
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.5%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 4.0.0 depends
MASS * imports
MRMix * imports
MRPRESSO * imports
MendelianRandomization * imports
RadialMR * imports
car * imports
cowplot * imports
data.table * imports
dplyr * imports
ggplot2 * imports
glmnet * imports
gridExtra * imports
gtable * imports
ieugwasr >= 0.1.5 imports
knitr * imports
lattice * imports
magrittr * imports
meta * imports
mr.raps * imports
pbapply * imports
plyr * imports
psych * imports
reshape2 * imports
rmarkdown * imports
Cairo * suggests
MRInstruments * suggests
markdown * suggests
randomForest * suggests
testthat * suggests

.github/workflows/check-full.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 4.1.4 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-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

twosamplemr

Science Score: 62.0%

Repository

Basic Info

Statistics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

proxy.golang.org: github.com/MRCIEU/TwoSampleMR

Rankings

proxy.golang.org: github.com/mrcieu/twosamplemr

Rankings

Dependencies