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
Links to: nature.com -
○Academic email domains
-
✓Institutional organization owner
Organization douglaslab has institutional domain (bionano.ucsf.edu) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.1%) to scientific vocabulary
Repository
DNA Origami TEM data analysis package
Basic Info
- Host: GitHub
- Owner: douglaslab
- License: mit
- Language: Python
- Default Branch: master
- Size: 472 KB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 7
- Releases: 0
Metadata Files
README.md
cryoorigami
DNA Origami Goniometer assisted cryoEM data analysis package. Python scripts and classes in this package can be used for other cryo-EM projects. Please cite DNA Origami Goniometers if you use this python package for your work.
Dependencies
- Relion
- Python 3.5 or above.
Installation
Installing this package inside python virtual environment is high encouraged. After installing virtualenv and virtualenvwrapper, create a python3 virtual environnment.
$mkvirtualenv em -p python3.
Remember to activate the virtualenvironment
$workon em
For most up to date version of the package, clone or download. Inside the cryoorigami package folder, execute
$(em) pip install .
If you would like to run the scripts in any path, make sure to add the bin folder in $PATH variable in your .bash_profile or .bashrc file.
Descriptions for commonly used scripts
For usage type em_***.py -h
em_addstarcols.py: Add new columns to a star file.
em_align2D.py: Align particles from 2D classification output to a reference class average.
em_alignclassaverages.py: Align class averages to a single class.
em_cistempars.py: Estimate cistem parameters for manual refinement run.
em_dfsc: Calculate directional fsc.
em_csparc2star: Convert csparc files to star file.
em_par2star: Convert par file to star.
em_stackcreate.py: Create particle stack from star file.
em_subtract2D.py: Subtract from particle images.
em_plotfsc.py: Plot FSC curve from xml data file.
em_plotstar.py: Plot star file data.
© 2020 Tural Aksel
Owner
- Name: Douglas Lab
- Login: douglaslab
- Kind: organization
- Email: shawn.douglas@ucsf.edu
- Location: San Francisco, CA
- Website: bionano.ucsf.edu
- Repositories: 25
- Profile: https://github.com/douglaslab
UCSF
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Aksel
given-names: Tural
orcid: https://orcid.org/0000-0002-8477-557X
title: "Cryoorigami: Data analysis tools for DNA Origami assisted cryo-EM studies"
version: 1.0.0
doi: 10.1038/s41587-020-0716-8
date-released: 2020-10-19
GitHub Events
Total
Last Year
Dependencies
- PyYAML ==5.4
- Pygments ==2.7.4
- matplotlib ==3.1.2
- mrcfile ==1.1.0
- numba ==0.42.0
- numpy ==1.17.4
- packaging ==19.2
- pandas ==0.25.3
- parso ==0.5.1
- pexpect ==4.7.0
- pickleshare ==0.7.5
- prompt-toolkit ==3.0.2
- ptyprocess ==0.6.0
- pyFFTW ==0.11.1
- pyparsing ==2.4.5
- python-dateutil ==2.8.1
- pytz ==2019.3
- scipy ==1.2.0
- sip ==5.0.0
- six ==1.13.0
- termcolor ==1.1.0
- toml ==0.10.0
- traitlets ==4.3.3
- wcwidth ==0.1.7
- PyYAML ==5.4
- Pygments ==2.7.4
- matplotlib ==3.1.2
- mrcfile ==1.1.0
- numba ==0.42.0
- numpy ==1.17.4
- packaging ==19.2
- pandas ==0.25.3
- parso ==0.5.1
- pexpect ==4.7.0
- pickleshare ==0.7.5
- prompt-toolkit ==3.0.2
- ptyprocess ==0.6.0
- pyFFTW ==0.11.1
- pyparsing ==2.4.5
- python-dateutil ==2.8.1
- pytz ==2019.3
- scipy ==1.2.0
- sip ==5.0.0
- six ==1.13.0
- termcolor ==1.1.0
- toml ==0.10.0
- traitlets ==4.3.3
- wcwidth ==0.1.7