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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://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
http://liorkirsch.github.io/brain-heatmap-web/
Custom Brain Heatmaps on top of the Allen Brain Atlas. Platform to generate brain heatmaps for the human or mouse brain ontop of the Allen Brain Atlas by editing google spreadsheet template with specific brain region and gene information.
Proper citation: Brain heatmap (RRID:SCR_023815) Copy
Software analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate variety of analyses pertaining to gene expression , chromatin accessibility, and their linkage. Used to perform analyses that link chromatin accessibility and GEX.
Proper citation: Cell Ranger ARC (RRID:SCR_023897) 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
Platform for data discovery to enhance the reuse of clinical neuroscience and neuroimaging data. Provides NeuroBridge ontology, and combines machine learning with ontology based search of both neuroimaging repositories like XNAT databases and open access full text journals such as PubMed Central. Connects researchers with potential neuroimaging data, by searching text of papers describing neuroimaging studies that contain information on neuroimaging data.
Proper citation: NeuroBridge (RRID:SCR_023703) Copy
https://www.cia.gov/the-world-factbook/about/
Presents basic realities about world in which we live in and is one of the U.S. Government’s most accessed publications. Provides basic intelligence on history, people, government, economy, energy, geography, environment, communications, transportation, military, terrorism, and transnational issues for 266 world entities.
Proper citation: The World Factbook (RRID:SCR_023548) Copy
http://fair.dei.unipd.it/software/
Software platform for integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA investigates correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas in order to create comprehensive, integrated data platform.
Proper citation: Multimodal Environment for Neuroimaging and Genomic Analysis (RRID:SCR_023822) 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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