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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.
Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.
Proper citation: QuPath (RRID:SCR_018257) Copy
https://github.com/taborlab/FlowCal
Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.
Proper citation: FlowCal (RRID:SCR_018140) Copy
https://github.com/ComparativeGenomicsToolkit/hal/tree/master/synteny
Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment.
Proper citation: halSynteny (RRID:SCR_018127) Copy
https://metacpan.org/dist/Bio-EUtilities
Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic.
Proper citation: Bio-EUtilities (RRID:SCR_024064) Copy
https://metacpan.org/dist/Bio-Tools-Run-Alignment-Clustalw
Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.
Proper citation: Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) Copy
https://metacpan.org/dist/Bio-Tools-Phylo-PAML
Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.
Proper citation: Bio-Tools-Phylo-PAML (RRID:SCR_024069) Copy
https://metacpan.org/dist/Bio-Graphics
Software package to generate GD images of Bio::Seq objects.
Proper citation: Bio-Graphics (RRID:SCR_024061) Copy
https://github.com/PacificBiosciences/pbcopper
Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications.
Proper citation: pbcopper (RRID:SCR_024152) Copy
https://github.com/genouest/biomaj-cli
Software package to use BioMAJ providing biomaj-cli.
Proper citation: CLI for BioMAJ (RRID:SCR_023980) Copy
Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution.
Proper citation: BCALM 2 (RRID:SCR_023975) Copy
https://github.com/gpertea/gclib
Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time.
Proper citation: GCLib (RRID:SCR_024028) Copy
Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies.
Proper citation: CAT and BAT (RRID:SCR_023988) Copy
https://github.com/RoelofBerg/limereg
Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image.
Proper citation: limereg (RRID:SCR_024097) Copy
https://github.com/xdf-modules/libxdf
Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications.
Proper citation: Libxdf (RRID:SCR_024096) 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://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/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
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