Comp Genomics Class
Code and examples for JHU Computational Genomics class
| 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. | ||||||||||
| Getting Started With Genomics Tools And Resources | 991 | 3 months ago | 1 | Shell | ||||||
| Unix, R and python tools for genomics and data science | ||||||||||
| Adam | 966 | 20 | 17 | 3 months ago | 14 | December 16, 2020 | 35 | apache-2.0 | Scala | |
| ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed. | ||||||||||
| Sarek | 299 | 3 months ago | 180 | mit | Nextflow | |||||
| Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing | ||||||||||
| Fgbio | 292 | 3 months ago | 16 | May 16, 2023 | 110 | mit | Scala | |||
| Tools for working with genomic and high throughput sequencing data. | ||||||||||
| Truvari | 284 | 10 days ago | 23 | August 07, 2023 | mit | Python | ||||
| Structural variant toolkit for VCFs | ||||||||||
| Htsjdk | 271 | 170 | 87 | 4 months ago | 78 | October 13, 2023 | 303 | Java | ||
| A Java API for high-throughput sequencing data (HTS) formats. | ||||||||||
| Sequenceserver | 259 | 1 | 3 months ago | 68 | October 05, 2023 | 91 | agpl-3.0 | JavaScript | ||
| Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!) | ||||||||||
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Jupyter Notebook
Genomics
Sequencing
Dna