Difference between revisions of "Free Software Directory:COVID-19 Response Team"
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*** https://tracker.debian.org/pkg/genometools | *** https://tracker.debian.org/pkg/genometools | ||
*** https://directory.fsf.org/wiki/Genometools | *** https://directory.fsf.org/wiki/Genometools | ||
| + | ** https://pysam.readthedocs.io/en/latest/ | ||
| + | ** Pysam is a python module for reading, manipulating and writing genomic data sets.Pysam is a wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing.This module provides a low-level wrapper around the htslib C-API as using cython and a high-level, pythonic API for convenient access to the data within genomic file formats. | ||
| + | *** https://tracker.debian.org/pkg/python-pysam | ||
| + | *** https://directory.fsf.org/wiki/Pysam | ||
| + | *** https://github.com/pysam-developers/pysam | ||
[[Category:Project Team]] | [[Category:Project Team]] | ||
Revision as of 12:40, 10 April 2020
About the Covid-19 Medical Group
Team Captain: David Hedlund
Participants:
- Donaldr3
- Mertgor
- Craigt
- Summary: An incident response team dedicated work on medical software relevant to COVID-19, and COVID-19 3D printing files.
Free 3D-printing files
Free software
- https://github.com/jakobzhao/virus/ - https://hgis.uw.edu/virus/
- https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6 - https://github.com/CSSEGISandData/COVID-19
- https://libreplanet.org/wiki/HACKERS_and_HOSPITALS#Software - thomzane's work on covid-19 resources
- https://www.gezapig.nl/covid.html - list put together by bendikker on health related free software
- https://wiki.debian.org/DebianMed
- https://wiki.debian.org/DebianMed/SoftwareLiberation
- https://pydicom.github.io/
- Dicom (Digital Imaging in Medicine) is the bread and butter of medical image datasets, storage and transfer.
- https://www.commonwl.org/
- The Common Workflow Language (CWL) is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, High Energy Physics, and Machine Learning.
- http://genometools.org/
- The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
- https://pysam.readthedocs.io/en/latest/
- Pysam is a python module for reading, manipulating and writing genomic data sets.Pysam is a wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing.This module provides a low-level wrapper around the htslib C-API as using cython and a high-level, pythonic API for convenient access to the data within genomic file formats.
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