VERSO
Viral Evolution ReconStructiOn (VERSO). The manuscript of the method is available at: https://www.cell.com/patterns/fulltext/S2666-3899(21)00022-2
Science Score: 13.0%
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Repository
Viral Evolution ReconStructiOn (VERSO). The manuscript of the method is available at: https://www.cell.com/patterns/fulltext/S2666-3899(21)00022-2
Basic Info
- Host: GitHub
- Owner: BIMIB-DISCo
- Language: R
- Default Branch: VERSO
- Homepage: https://bimib-disco.github.io/VERSO/
- Size: 3.65 MB
Statistics
- Stars: 7
- Watchers: 4
- Forks: 4
- Open Issues: 0
- Releases: 9
Metadata Files
README.md
Viral Evolution ReconStructiOn (VERSO)
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In this repository we provide an implementation of the VERSO (Viral Evolution ReconStructiOn) framework.
VERSO is an algorithmic framework that processes variants profiles from viral samples, to produce phylogenetic models of viral evolution from clonal variants and to subsequently quantify the intra-host genomic diversity of samples. VERSO includes two separate and subsequent steps, which are perfomed via the scripts provided in this repository.
The manuscript of the method is available at this link: https://www.cell.com/patterns/fulltext/S2666-3899(21)00022-2
VERSO STEP #1: robust phylogenomic inference from clonal variant profiles
VERSO STEP #1 employs a probabilistic maximum-likelihood framework for the reconstruction of robust phylogenetic trees from binarized mutational profiles of clonal variants.
VERSO STEP #1 takes as input: a n (samples) × m (variants) binary mutational profile matrix, as defined on clonal SNVs only. In this case, an entry in a given sample is equal to 1 (present) if the VF is larger than a certain threshold (in our analyses, equal to 90%), it is equal to 0 if lower than a distinct threshold (in our analyses, equal to 5%), and is considered as missing (NA) in the other cases.
VERSO outputs: (i) a phylogenetic model where each leaf correspond to a sample, whereas internal nodes correspond to accumulating clonal variants (in Newick format), (ii) the corrected clonal genotype of each sample.
VERSO is provided as an R open source tool.
RUNNING
To run the VERSO STEP #1 tool please go to the folder: https://github.com/BIMIB-DISCo/VERSO/tree/VERSO/VERSOSTEP1 and refer to the related readme, which includes instructions and guidelines.
VERSO STEP #2: characterization of intra-host genomic diversity
In the second step, VERSO takes into account the variant frequency profiles of groups of samples with the same clonal genotype (identified via VERSO STEP #1), in order to characterize their intra-host genomic diversity and visualize it on a low-dimensional space.
VERSO STEP #2 takes as input a n (samples) × m (variants) variant frequency (VF) profile matrix, in which each entry includes the VF ∈ (0,1) of a given mutation in a certain sample, after filtering out: (i) the clonal variants employed in STEP #1 and (ii) the minor variants possibly involved in homoplasies.
As output, VERSO STEP #2 delivers both the partitioning of samples in homogeneous clusters and the visualizationin a low-dimensional space, also allowing to label samples according to other covariates, such as, e.g., collection date or geographical location.
VERSO STEP #2 is provided as a Python script which employs the SCANPY suite of tools.
RUNNING
To run the VERSO STEP #2 tool please go to the folder: https://github.com/BIMIB-DISCo/VERSO/tree/VERSO/VERSOSTEP2 and refer to the related readme, which includes instructions and guidelines.
CONTACTS
Please feel free to contact us if you have problems running our tool at daniele.ramazzotti1@gmail.com or d.maspero@campus.unimib.it.
Owner
- Name: Data and Computational Biology Group UNIMIB (was BI*oinformatics MI*lan B*icocca)
- Login: BIMIB-DISCo
- Kind: organization
- Website: http://dcb.disco.unimib.it
- Repositories: 10
- Profile: https://github.com/BIMIB-DISCo
The github organization of the DCB group of the DISCo, Università degli Studi di Milano Bicocca
GitHub Events
Total
- Release event: 1
- Push event: 8
Last Year
- Release event: 1
- Push event: 8
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| danro9685 | d****i@y****m | 56 |
| alexgraudenzi | a****i@u****t | 55 |
| DavideMaspero | d****o@c****t | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 4
- Total pull requests: 4
- Average time to close issues: about 17 hours
- Average time to close pull requests: 4 days
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 1.25
- Average comments per pull request: 0.0
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
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- Average time to close pull requests: N/A
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- Pull request authors: 0
- Average comments per issue: 0
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- Merged pull requests: 0
- Bot issues: 0
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Top Authors
Issue Authors
- AndreaAguadoM (4)
Pull Request Authors
- luca-dex (4)
Top Labels
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Packages
- Total packages: 1
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Total downloads:
- bioconductor 7,518 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: VERSO
Viral Evolution ReconStructiOn (VERSO)
- Homepage: https://github.com/BIMIB-DISCo/VERSO
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/VERSO/inst/doc/VERSO.pdf
- License: file LICENSE
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Latest release: 1.18.0
published over 1 year ago