Science Score: 20.0%
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
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: biorxiv.org -
✓Committers with academic emails
4 of 11 committers (36.4%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.3%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Tools for manipulating annotated data matrices
Basic Info
Statistics
- Stars: 93
- Watchers: 19
- Forks: 35
- Open Issues: 11
- Releases: 0
Topics
Metadata Files
README.md
cmapR (CMap R code)
Parsing and utility functions for analyzing CMap data. To learn more about the CMap project at the Broad Institute, please visit clue.io.
NOTICE - Updates for Bioconductor
cmapR has been accepted in Bioconductor. In accordance with Bioconductor standards, we have changed some of the function naming conventions. Function names that used to contain . have been replaced with _. Hence, parse.gctx is now parse_gctx and so on. The older function names will still work with a warning. There is additional info and examples in the vignettes/tutorial.Rmd.
Install instructions
Installing from Bioconductor
In R version 4.0 or newer:
``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("cmapR") ```
Dependencies are listed in DESCRIPTION
Docker
A docker container with a slightly earlier version of cmapR can be obtained here: https://hub.docker.com/r/cmap/cmapr. This may be preferable for those who would like to use the package without installing on their system.
Installing from Github source
Perhaps the simplest way to install directly from github is using devtools::install_github("cmap/cmapR"). Note that this requires having previously installed the devtools package.
The script install_cmapR.R takes care of installing all the dependencies and then running devtools::install_github("cmap/cmapR"), so you can simply source this script after cloning this repository.
Alternatively, you can point your R's install.packages function at a tarball of the cmapR archive. You can generate this archive by cloning this repository and doing the following:
# make a gzip tar ball of the repo
R CMD build cmapR
# makes cmapR_1.0.tar.gz
# check that the package is ok
R CMD check cmapR_1.0.tar.gz
Once you have created the tarball, open an R terminal and execute the following:
install.packages("cmapR_1.0.tar.gz", type="source", repos=NULL)
library("cmapR")
You can also source individual files as needed instead of installing the entire package.
# For example, just load the IO methods
source("cmapR/R/io.R")
Citation information
If you use GCTx and/or cmapR in your work, please cite Enache et al.
Owner
- Name: Connectivity Map at the Broad Institute
- Login: cmap
- Kind: organization
- Email: clue@broadinstitute.org
- Location: Cambridge, MA 02142
- Website: https://clue.io
- Repositories: 38
- Profile: https://github.com/cmap
Helping drug discovery, one signature at a time
GitHub Events
Total
- Issues event: 2
- Watch event: 8
- Issue comment event: 4
Last Year
- Issues event: 2
- Watch event: 8
- Issue comment event: 4
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Ted Natoli | t****i@g****m | 196 |
| jasiedu | j****u@b****g | 9 |
| Nitesh Turaga | n****a@g****m | 6 |
| Oana Enache | o****e@g****m | 6 |
| Oana Enache | o****a@b****g | 5 |
| Mike Smith | g****h@g****m | 2 |
| Darío Hereñú | m****a@g****m | 2 |
| Janani Ravi | j****i@m****u | 1 |
| Nuno Agostinho | n****o@g****m | 1 |
| OganM | o****i@g****m | 1 |
| dedavison | d****n@b****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 55
- Total pull requests: 33
- Average time to close issues: 6 months
- Average time to close pull requests: 3 days
- Total issue authors: 38
- Total pull request authors: 7
- Average comments per issue: 3.2
- Average comments per pull request: 0.15
- Merged pull requests: 33
- 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: 2.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- tnat1031 (10)
- luyoutao (2)
- enricoferrero (2)
- afaissa (2)
- antonkratz (2)
- XiaohanChen97 (2)
- cyk64 (1)
- nzllim (1)
- Jimmay13 (1)
- sherrybaker1119 (1)
- vjcitn (1)
- ge2sasag (1)
- jjyotikataria (1)
- erikfel97 (1)
- tapiocaaaa (1)
Pull Request Authors
- tnat1031 (16)
- kant (2)
- jananiravi (1)
- oganm (1)
- grimbough (1)
- nuno-agostinho (1)
- oena (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 34,430 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: cmapR
CMap Tools in R
- Homepage: https://github.com/cmap/cmapR
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/cmapR/inst/doc/cmapR.pdf
- License: file LICENSE
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Latest release: 1.20.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.0 depends
- SummarizedExperiment * imports
- data.table * imports
- flowCore * imports
- matrixStats * imports
- methods * imports
- rhdf5 * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests