Haplotyped Methylome
Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
| Project Name | Stars | Downloads | Repos Using This | Packages Using This | Most Recent Commit | Total Releases | Latest Release | Open Issues | License | Language |
|---|---|---|---|---|---|---|---|---|---|---|
| Deepvariant | 2,978 | 4 months ago | 8 | bsd-3-clause | Python | |||||
| DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. | ||||||||||
| Gatk | 1,576 | 2 | a month ago | 46 | March 16, 2023 | 1,299 | other | Java | ||
| Official code repository for GATK versions 4 and up | ||||||||||
| Galaxy | 1,211 |  | 2 | 23 | 3 months ago | 30 | December 08, 2023 | 2,169 | other | Python |
| Data intensive science for everyone. | ||||||||||
| Htsjdk | 271 | 170 | 87 | 4 months ago | 78 | October 13, 2023 | 303 | Java | ||
| A Java API for high-throughput sequencing data (HTS) formats. | ||||||||||
| Shasta | 269 | 2 years ago | other | C++ | ||||||
| [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads | ||||||||||
| Comp Genomics Class | 236 | 3 years ago | 4 | gpl-2.0 | Jupyter Notebook | |||||
| Code and examples for JHU Computational Genomics class | ||||||||||
| Pycoqc | 213 | 5 months ago | 50 | December 16, 2020 | 14 | gpl-3.0 | Python | |||
| pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy) | ||||||||||
| Ugene | 190 | 3 months ago | 6 | gpl-2.0 | C++ | |||||
| UGENE is free open-source cross-platform bioinformatics software | ||||||||||
| Nextclade | 190 |  | 2 | 3 months ago | 52 | April 27, 2022 | 154 | mit | TypeScript | |
| Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement | ||||||||||
| Genomics | 154 | 2 years ago | 2 | R | ||||||
| A collection of scripts and notes related to genomics and bioinformatics | ||||||||||
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