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GSR: Simulator - FreeHi-C
| Attribute | Value |
|---|---|
| Title | FreeHi-C |
| Short Description | FreeHi-C simulates high fidelity Hi-C data for benchmarking and data augmentation |
| Long Description | FreeHi-C (v2.0) is short for Fragment interactions empirical estimation for fast simulation of Hi-C data. It is a data-driven Hi-C data simulator for simulating and augmenting Hi-C datasets. FreeHi-C employs a non-parametric strategy for estimating an interaction distribution of genome fragments and simulates Hi-C reads from interacting fragments. Data from FreeHi-C exhibit higher fidelity to the biological Hi-C data. FreeHi-C not only can be used to study and benchmark a wide range of Hi-C analysis methods but also boosts power and enables false discovery rate control for differential interaction detection algorithms through data augmentation. Different from FreeHi-C (v1.0), a spike-in module is added enabling the simulation of true differential chromatin interactions. FreeHi-C is designed for studies that are prone to simulate Hi-C interactions from the real data and add deviations from the true ones. Therefore, FreeHi-C requires real Hi-C sequencing data (FASTQ format) as input along with user-defined simulation parameters. FreeHi-C will eventually provide the simulated genomics contact counts in a sparse matrix format (BED format) which is compatible with the standard input of downstream Hi-C analysis. |
| Keywords | high-throughput chromatin conformation, Hi-C, differential chromatin interaction detection, |
| Version | 2.0 |
| Project Started | 2019 |
| Last Release | 4 years, 3 months ago |
| Homepage | https://github.com/yezhengSTAT/FreeHiC |
| Citations | Zheng Y, Keleş S, FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation., Nat Methods, Jan. 1, 2020 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | Sept. 28, 2022 (1082 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | |
| Variations | |
| Simulation Method | |
| Input | |
| Data Type | Empirical, |
| File format | Other, |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | Other, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | |
| Development | |
| Tested Platforms | |
| Language | C or C++, Python, |
| License | MIT, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using FreeHi-C has been provided.
Please propose new citations if you are aware of publications that use this software.