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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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Mspire-Simulator Resource Report Resource Website 1+ mentions |
Mspire-Simulator (RRID:SCR_001431) | standalone software, software application, simulation software, software resource | A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components. | standalone software, shotgun, proteomic, simulation software, bio.tools |
uses: mzML is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: Brigham Young University; Utah; USA |
PMID:24090032 | Free, Freely Available | biotools:mspire-simulator, OMICS_03359 | https://bio.tools/mspire-simulator | SCR_001431 | 2026-08-06 09:25:23 | 1 | |||||||
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Populations Resource Report Resource Website |
Populations (RRID:SCR_024175) | software library, software toolkit, software resource | Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions. | Population genetic, individuals or populations distances, allelic frequencies, phylogenetic trees, file conversions, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29592 | https://sources.debian.org/src/populations/ | SCR_024175 | populations | 2026-08-06 09:30:17 | 0 | |||||||
|
quicktree Resource Report Resource Website 10+ mentions |
quicktree (RRID:SCR_024205) | software library, software toolkit, software resource | Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments. | Neighbor-Joining algorithm, reconstructing phylogenies from huge alignments, | is listed by: Debian | PMID:3447015 | Free, Available for download, Freely available, | https://sources.debian.org/src/quicktree/ | SCR_024205 | 2026-08-06 09:30:20 | 12 | ||||||||
|
python-airr Resource Report Resource Website |
python-airr (RRID:SCR_024187) | software library, software toolkit, software resource | Software airr reference library provides basic functions and classes for interacting with AIRR Community Data Representation Standards, including tools for read, write and validation. | airr reference library, functions and classes for interacting with AIRR Community Data Representation Standards, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-airr/ | SCR_024187 | 2026-08-06 09:30:16 | 0 | |||||||||
|
Tab2MAGE Resource Report Resource Website |
Tab2MAGE (RRID:SCR_024101) | software library, software toolkit, software resource | Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange. | ArrayExpress, submitting large microarray experiment datasets, spreadsheet format for MIAME annotation of microarray experiments, | is listed by: Debian | Free, Available for download, Freely available, | https://tab2mage.sourceforge.net/ | https://sources.debian.org/src/mage2tab/ | SCR_024101 | mage2tab, ArrayExpress Tab2MAGE | 2026-08-06 09:30:15 | 0 | |||||||
|
Mapsembler2 Resource Report Resource Website 1+ mentions |
Mapsembler2 (RRID:SCR_024102) | software library, software toolkit, software resource | Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants. | Targeted assembly, NGS raw read, input sequences, | is listed by: Debian | PMID:22443449 | Free, Available for download, Freely available, | OMICS_18310 | https://sources.debian.org/src/mapsembler2/ | SCR_024102 | mapsembler2, Mapsembler | 2026-08-06 09:30:19 | 1 | ||||||
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affyio Resource Report Resource Website |
affyio (RRID:SCR_024223) | software library, software toolkit, software resource | Software R package as routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing CEL and CDF file formats. | parsing Affymetrix data files, accessing CEL and CDF file formats, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29381 | https://sources.debian.org/src/r-bioc-affyio/ | SCR_024223 | 2026-08-06 09:30:21 | 0 | ||||||||
|
MAXFLOW Resource Report Resource Website |
MAXFLOW (RRID:SCR_024103) | software library, software toolkit, software resource | Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph. | computing mincut/maxflow in a graph, | is listed by: Debian | DOI:10.1109/TPAMI.2004.60 | Free, Available for download, Freely available, | https://sources.debian.org/src/maxflow/ | SCR_024103 | maxflow | 2026-08-06 09:30:15 | 0 | |||||||
|
pssh2 Resource Report Resource Website |
pssh2 (RRID:SCR_024181) | software library, software toolkit, software resource | Software tools for creating the sequence-to-structure alignment database PSSH2. | creating sequence-to-structure alignment database, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pssh2/ | SCR_024181 | 2026-08-06 09:30:20 | 0 | |||||||||
|
pyepl Resource Report Resource Website 1+ mentions |
pyepl (RRID:SCR_024182) | software library, software toolkit, software resource | Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses. | coding psychology experiments, Python | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/python-pyepl/ | SCR_024182 | Python Experiment-Programming Library | 2026-08-06 09:30:16 | 3 | ||||||||
|
pbcopper Resource Report Resource Website |
pbcopper (RRID:SCR_024152) | software library, software toolkit, software resource | Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications. | data structures, algorithms, utilities for PacBio C++ applications, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pbcopper/ | SCR_024152 | 2026-08-06 09:30:16 | 0 | |||||||||
|
Parsnp Resource Report Resource Website 10+ mentions |
Parsnp (RRID:SCR_024153) | software library, software toolkit, software resource | Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction. | align core genome, bacterial genomes, | is listed by: Debian | PMID:25410596 | Free, Available for download, Freely available, | OMICS_21461 | https://sources.debian.org/src/parsnp/, https://github.com/marbl/parsnp | SCR_024153 | parsnp | 2026-08-06 09:30:20 | 39 | ||||||
|
PDB2PQR Resource Report Resource Website 1+ mentions |
PDB2PQR (RRID:SCR_024155) | software library, software toolkit, software resource | Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files. | interface for running PDB2PQR web service, prepare structures for further calculations, reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, generating PQR files, | is listed by: Debian | PMID:17488841 | Free, Available for download, Freely available, | OMICS_14370 | https://sources.debian.org/src/pdb2pqr/ | SCR_024155 | pdb2pqr | 2026-08-06 09:30:16 | 2 | ||||||
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PfTools Resource Report Resource Website 1+ mentions |
PfTools (RRID:SCR_024158) | software library, software toolkit, software resource | Software suite of tools to build and search generalized profiles. | build and search generalized profiles, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29588 | https://sources.debian.org/src/pftools/ | SCR_024158 | pftools | 2026-08-06 09:30:16 | 2 | |||||||
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PhySamp Resource Report Resource Website 1+ mentions |
PhySamp (RRID:SCR_024159) | software library, software toolkit, software resource | Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree. | phylogenetic sampling, sample sequence alignment, corresponding phylogenetic tree, | is listed by: Debian | PMID:26055961 | Free, Available for download, Freely available, | OMICS_21686 | https://sources.debian.org/src/physamp/ | SCR_024159 | physamp | 2026-08-06 09:30:20 | 1 | ||||||
|
GCLib Resource Report Resource Website |
GCLib (RRID:SCR_024028) | software library, software toolkit, software resource | 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. | reusable code for bioinformatics, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/gclib/ | SCR_024028 | gclib, genome-code-lib | 2026-08-06 09:30:14 | 0 | ||||||||
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ParsInsert Resource Report Resource Website |
ParsInsert (RRID:SCR_024163) | software library, software toolkit, software resource | Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. | Parsimonious Insertion, unclassified sequences, phylogenetic tree, produce phylogenetic tree, produce taxonomic classification, produce sequences, microbial community sequence analysis, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21460 | https://sources.debian.org/src/parsinsert/ | SCR_024163 | parsinsert | 2026-08-06 09:30:20 | 0 | |||||||
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python-bx Resource Report Resource Website 10+ mentions |
python-bx (RRID:SCR_024202) | software library, software toolkit, software resource | Software Python library and associated set of scripts for rapid implementation of genome scale analyses. | rapid implementation of genome scale analyses, | is listed by: Debian | OMICS_18239 | https://sources.debian.org/src/python3-bx/ | SCR_024202 | 2026-08-06 09:30:20 | 24 | |||||||||
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limereg Resource Report Resource Website |
limereg (RRID:SCR_024097) | software library, software toolkit, software resource | 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. | 2D, rigid image registration, greyscale images, transformation parameters, registered image, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/limereg/ | SCR_024097 | 2026-08-06 09:30:15 | 0 | |||||||||
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NeoBio Resource Report Resource Website |
NeoBio (RRID:SCR_024131) | software library, software toolkit, software resource | Software library of sequence alignment algorithms implemented in Java. | bioinformatics algorithms implemented in Java, sequence alignment algorithms, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21450 | https://sources.debian.org/src/neobio/ | SCR_024131 | neobio | 2026-08-06 09:30:16 | 0 |
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