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https://github.com/Washington-University/CiftiLib
Software C++ Library for reading and writing CIFTI-2 and CIFTI-1 files.
Proper citation: CiftiLib (RRID:SCR_023996) Copy
https://github.com/rvaser/bioparser/
Software C++ library for parsing several formats in bioinformatics. C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.
Proper citation: Bioparser (RRID:SCR_024065) Copy
Software memory efficient bioinformatics library written in D programming language whose aim is to provide platform for developing high performance computational biology applications using the D programming language through automatic parallelization of tasks where possible and by avoiding unnecessary memory allocations.
Proper citation: BioD (RRID:SCR_024062) Copy
https://github.com/IRCAD-IHU/camp
Software multi-purpose reflection library developped by Technogerma Systems France and then by Tegesoft. Provides extra layer of flexibility to programs, and allows them to fully expose their data structures at runtime.
Proper citation: CAMP (RRID:SCR_023981) Copy
https://github.com/ggonnella/gfapy
Software library for handling sequence graphs in Python.
Proper citation: GfaPy (RRID:SCR_024030) Copy
Software package for analyzing, processing and visualizing multi-dimensional microscopy images. Multipurpose postprocessing tool for bioimaging. Can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once.
Proper citation: BioImageXD (RRID:SCR_023979) Copy
Software application as simultaneous Bayesian inference of alignment and phylogeny. Used to estimate multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. to explore the joint space of alignment and phylogeny given molecular sequence data. BAli-Phy version 3 is model based co-estimation of alignment and phylogeny. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. Implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously.
Proper citation: BAli-Phy (RRID:SCR_023976) Copy
https://github.com/intake/intake
Software package for finding, investigating, loading and disseminating data.
Proper citation: Intake (RRID:SCR_024042) Copy
https://ismrmrd.github.io/apidocs/1.5.0/
Prerequisite for sharing magnetic resonance imaging reconstruction algorithms and code is a common raw data format. This repository describes such common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. The repository also contains a C/C++ library for working with the format.
Proper citation: ISMRMRD (RRID:SCR_024043) Copy
https://github.com/andersen-lab/ivar
Software package for viral amplicon based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.Contains intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.Following functions are implemented in iVar: trimming of primers and low-quality bases; consensus calling; variant calling both iSNVs and insertions/deletions; identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.
Proper citation: iVar (RRID:SCR_024045) Copy
https://changeo.readthedocs.io
Collection of software tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, and reconstructing germline sequences.
Proper citation: Change-O (RRID:SCR_023986) Copy
Open Source software modular Java libraries for cheminformatics.
Proper citation: CDK (RRID:SCR_023985) Copy
https://github.com/gramos/imagetooth
Software library to generate images for odontograms.Allows to choose between png or jpg images.
Proper citation: ImageTooth (RRID:SCR_024039) Copy
https://github.com/rdpstaff/TaxonomyTree
Software library used by other RDP tools.TaxonomyTree building and traversal utility classes.
Proper citation: TaxonomyTree (RRID:SCR_024090) Copy
https://metacpan.org/dist/Sort-Key-Top
Functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures.
Proper citation: Sort-Key-Top (RRID:SCR_024092) Copy
https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen
Software library as set of classes for creating statistical genetic programs.
Proper citation: libStatGen (RRID:SCR_024093) Copy
https://github.com/rvaser/thread_pool
Software C++ thread pool library.
Proper citation: ThreadPool (RRID:SCR_024094) Copy
https://opencfu.sourceforge.net/
Software to count cell colonies and other circular objects. Used to facilitate enumeration of colony forming unit.
Proper citation: OpenCFU (RRID:SCR_024142) Copy
https://github.com/GATB/gatb-core
Software genome analysis toolbox with de-Bruijn graph. Library dedicated to genome assembly and analysis.
Proper citation: GATB (RRID:SCR_024024) Copy
https://github.com/rizkg/BBHash
Software library for building minimal perfect hash function. Designed to handle large scale datasets.
Proper citation: BBHash (RRID:SCR_023972) Copy
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