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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.aquamaniac.de/rdm/projects/libchipcard

Software library for generic access to chipcard readers and cards

Proper citation: Libchipcard (RRID:SCR_024071) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.commontk.org/

Software to support biomedical image computing.

Proper citation: CTK (RRID:SCR_024002) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/kdm9/libqes

Software C library with bioinformatic focus optimised for speed and clean API.

Proper citation: libqes (RRID:SCR_024083) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://pubcrawler.gen.tcd.ie/

PubCrawler is a free alerting service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases. PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests. The free PubCrawler web service has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short notifications or emails with the latest updates as soon as they become available. PubCrawler searches the NCBI PubMed (Medline) and Entrez (GenBank) databases daily using search parameters (keywords, author names, etc.) specified by the user. There is no limit on the number of searches that can be carried out. Previous search hits are stored and only the newest PubMed or GenBank records are shown each day. The results are presented as an HTML Web page, similar to the results of an NCBI PubMed or Entrez query. This Web page can be located on our computer (the PubCrawler WWW-Service), on your computer (the stand-alone program), or you can receive it via e-mail (set this up using the PubCrawler WWW-Service). The Web page sorts the results into groups of PubMed/GenBank entries that are zero-days-old, 1-day-old, 2-days-old, etc., up to a user-specified age limit. Sponsors: Development of PubCrawler was supported by EMBnet

Proper citation: PubCrawler (RRID:SCR_008235) Copy   

•   Source: SciCrunch Registry

http://biopython.org

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. It works along with the Open Bioinformatics Foundation, who generously host it''s website, bug tracker, and mailing lists. Sponsor: This resource is supported by the Open Bioinformatics Foundation. Keywords: Tool, Software, Python, Biological, Computation, Bioinformatics,

Proper citation: Biopython (RRID:SCR_007173) Copy   

•   Source: SciCrunch Registry

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https://cran.r-project.org/web/packages/adegenet/index.html

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

Proper citation: ADEGENET (RRID:SCR_000825) Copy   

•   Source: SciCrunch Registry

https://ccg.murdoch.edu.au/yabi/login/?next=/yabi/

A web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts.

Proper citation: Yabi (RRID:SCR_005359) Copy   

•   Source: SciCrunch Registry

http://neuro.debian.net/pkgs/cmtk.html

A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model). CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU). Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished.

Proper citation: Computational Morphometry Toolkit (RRID:SCR_002234) Copy   

•   Source: SciCrunch Registry

http://huttenhower.sph.harvard.edu/galaxy

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LEfSe (RRID:SCR_014609) Copy   

•   Source: SciCrunch Registry