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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://freeimage.sourceforge.io/
Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications.
Proper citation: FreeImage (RRID:SCR_024022) Copy
https://github.com/bioinfo-ut/GenomeTester4
Software toolkit for performing set operations - union, intersection and complement on k-mer lists.
Proper citation: GenomeTester4 (RRID:SCR_024026) Copy
GDCM includes file format definition and network communications protocol, both of which should be extended to provide full set of tools for researcher or small medical imaging vendor to interface with existing medical database.Implementation of DICOM standard designed to be open source so that researchers may access clinical data directly.
Proper citation: GDCM (RRID:SCR_024027) Copy
https://github.com/nextstrain/augur
Software package to track evolution from sequence and serological data. Provides collection of commands which are designed to be composable into larger processing pipelines.
Proper citation: Augur (RRID:SCR_023964) Copy
https://github.com/tjhladish/EpiFire/wiki
Open source C++ library and application for contact network epidemiology. Application programming interface that models the spread of infectious disease in population and generates and manipulates networks of nodes and edges.
Proper citation: EpiFire (RRID:SCR_024017) Copy
https://cme.h-its.org/exelixis/web/software/exabayes/
Software package for Bayesian tree inference. Used for large-scale analyses on computer clusters.
Proper citation: ExaBayes (RRID:SCR_024019) Copy
https://github.com/mbillingr/libgdf
Software library for processing of biomedical signals. Provides generic storage for biosignals, such as EEG, ECG, MEG. C++ implementation of GDF - " general dataformat for biosignals" version V2.20.
Proper citation: libGDF (RRID:SCR_024075) Copy
https://github.com/husonlab/jloda
Software Java library of data structures and algorithms.Provides some basic data structures and algorithms used by SplitsTree, Dendroscope and MEGAN.
Proper citation: JLODA (RRID:SCR_024076) Copy
https://gitlab.com/german.tischler/libmaus2
Software collection of data structures and algorithms. Contains I/O classes (single byte and UTF-8), bitio classes (input, output and various forms of bit level manipulation), text indexing classes (suffix and LCP array, fulltext and minute (FM), ...), BAM sequence alignment files input/output (simple and collating) and many lower level support classes.
Proper citation: libmaus2 (RRID:SCR_024077) Copy
https://www.aquamaniac.de/rdm/projects/libchipcard
Software library for generic access to chipcard readers and cards
Proper citation: Libchipcard (RRID:SCR_024071) Copy
https://github.com/vcflib/tabixpp
Software C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.Wrapper to tabix indexer
Proper citation: tabixpp (RRID:SCR_024107) Copy
https://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html
Software library that exports C++ mmCIF accessors to Python.
Proper citation: Core Wrapper (RRID:SCR_024087) Copy
https://github.com/brentp/cyvcf2
Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis.
Proper citation: cyvcf2 (RRID:SCR_024000) Copy
Software to support biomedical image computing.
Proper citation: CTK (RRID:SCR_024002) Copy
https://github.com/wdecoster/nanolyse
Software package to remove reads mapping to the lambda phage genome from a fastq file.
Proper citation: NanoLyse (RRID:SCR_024125) Copy
https://github.com/mtholder/ncl
Software C++ class library for interpreting data files in NEXUS format. NEXUS Class Library software package is collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses.NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored.
Proper citation: libncl (RRID:SCR_024080) Copy
https://github.com/kdm9/libqes
Software C library with bioinformatic focus optimised for speed and clean API.
Proper citation: libqes (RRID:SCR_024083) Copy
https://github.com/toddy15/medicalterms
Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words.
Proper citation: medicalterms (RRID:SCR_024117) Copy
https://www.bioinformatics.org/~tryphon/populations/
Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions.
Proper citation: Populations (RRID:SCR_024175) Copy
https://github.com/khowe/quicktree/
Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments.
Proper citation: quicktree (RRID:SCR_024205) Copy
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