https://github.com/cbg-ethz/sciphi
Science Score: 10.0%
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
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✓Committers with academic emails
5 of 9 committers (55.6%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.0%) to scientific vocabulary
Keywords from Contributors
Repository
Basic Info
- Host: GitHub
- Owner: cbg-ethz
- License: other
- Language: C++
- Default Branch: master
- Size: 769 KB
Statistics
- Stars: 25
- Watchers: 5
- Forks: 11
- Open Issues: 10
- Releases: 0
Metadata Files
README.md
SCIPhI
Description
Single-cell mutation identification via phylogenetic inference (SCIPhI) is a new approach to mutation detection in individual tumor cells by leveraging the evolutionary relationship among cells. SCIPhI, jointly calls mutations in each individual cell and estimates the tumor phylogeny on these cells. Employing a Markov Chain Monte Carlo scheme we robustly account for the various sources of noise in single-cell sequencing data. Our approach enables us to reliably call mutations in each single cell even in experiments with high dropout rates and missing data
Availability
SCIPhI is freely available under a GNU General Public License v3.0 at https://github/cbg-ETHZ/SCIPhI
How to install SCIPhI
SCIPhI has the following dependencies which need to be installed:
Boost >= 1.6.x,SeqAn >= 2.3.2,DLIB >= 19.9zlib
Clone SCIPhI with submodules from the soucre code:
git clone --recurse-submodules https://github.com/cbg-ethz/SCIPhI.git
In order to install SCIPhI issue the following commands in the github directory:
autoreconf -vif
./configure --with-boost=BOOST_PATH SEQAN_INCLUDEDIR=SEQAN_PATH DLIB_INCLUDEDIR=DLIB_PATH
make
An alternative is to use CMake (tested with version >= 3.11.1). Simply issue the commands:
mkdir build
cd build
cmake ..
cmake --build . --config Release
Afterwards you will find SCIPhI in the build directory.
Run SCIPhI
SCIPhI expects the sequencing information to be passed in form of the well known mpileup format (http://www.htslib.org/doc/samtools.html). In order to generate such a file you need to align your fastq files to a reference and post process the result (e.g., following the instuctions here: https://gatk.broadinstitute.org/hc/en-us/articles/360035535912-Data-pre-processing-for-variant-discovery).
In order to see all available options type
sciphi -h
Executing
sciphi -o result --in cellNames.txt --seed 42 example.mpileup
will run SCIPhI using the cell names provided in cellNames.txt (same order as in the mpileup file). Note that cellNames.txt is a tab delimited file with the cell name in the first column and a cell type identifier in the second column. The cell type can be either CT (tumor cell), CN (control normal cell), or BN (control bulk normal). Note that SCIPhI assumes a pileup against a reference and ignores positions with 'N' as reference.
Owner
- Name: Computational Biology Group (CBG)
- Login: cbg-ethz
- Kind: organization
- Location: Basel, Switzerland
- Website: https://www.bsse.ethz.ch/cbg
- Twitter: cbg_ethz
- Repositories: 91
- Profile: https://github.com/cbg-ethz
Beerenwinkel Lab at ETH Zurich
GitHub Events
Total
Last Year
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jochen Singer | s****j@l****h | 47 |
| singerj | s****j | 35 |
| Jochen Singer | s****j@l****h | 24 |
| Warren Kretzschmar | w****k@k****e | 7 |
| Jochen Singer | s****j@b****h | 3 |
| Jochen Singer | j****n@J****x | 2 |
| yechang | y****0@g****m | 1 |
| Warren Kretzschmar | w****r@k****e | 1 |
| Jochen Singer | j****n@s****h | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 19
- Total pull requests: 8
- Average time to close issues: 8 days
- Average time to close pull requests: 3 days
- Total issue authors: 12
- Total pull request authors: 3
- Average comments per issue: 2.58
- Average comments per pull request: 0.75
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- winni2k (4)
- singerj (3)
- biobenkj (2)
- boegel (1)
- tamaraprieto (1)
- amkozlov (1)
- buutrg (1)
- haochenz96 (1)
- jmfa (1)
- dpryan79 (1)
- Yingjie848 (1)
- armintoepfer (1)
Pull Request Authors
- singerj (4)
- winni2k (3)
- y9c (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
- Total downloads: unknown
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 14
proxy.golang.org: github.com/cbg-ethz/SCIPhI
- Documentation: https://pkg.go.dev/github.com/cbg-ethz/SCIPhI#section-documentation
- License: other
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Latest release: v0.1.7
published over 6 years ago
Rankings
proxy.golang.org: github.com/cbg-ethz/sciphi
- Documentation: https://pkg.go.dev/github.com/cbg-ethz/sciphi#section-documentation
- License: other
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Latest release: v0.1.7
published over 6 years ago