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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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Core Wrapper Resource Report Resource Website 1+ mentions |
Core Wrapper (RRID:SCR_024087) | software library, software resource, software toolkit | Software library that exports C++ mmCIF accessors to Python. | exports C++ mmCIF accessors to Python, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/librcsb-core-wrapper0-dev/ | SCR_024087 | CORE-WRAPPER, core-wrapper | 2026-02-17 10:04:36 | 1 | ||||||||
|
cyvcf2 Resource Report Resource Website 1+ mentions |
cyvcf2 (RRID:SCR_024000) | software library, software resource, software toolkit | 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. | files parsing and querying, VCF files, BCF files, | is listed by: Debian | PMID:28165109 | Free, Available for download, Freely available | OMICS_20006 | https://sources.debian.org/src/cyvcf2/ | SCR_024000 | 2026-02-17 10:04:32 | 2 | |||||||
|
CTK Resource Report Resource Website 1+ mentions |
CTK (RRID:SCR_024002) | software resource, software toolkit | Software to support biomedical image computing. | support biomedical image computing, biomedical image computing, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/libctk-dev/ | SCR_024002 | CTK - The Common Tool Kit, ctk | 2026-02-17 10:04:39 | 1 | ||||||||
|
NanoLyse Resource Report Resource Website 1+ mentions |
NanoLyse (RRID:SCR_024125) | software library, software resource, software toolkit | Software package to remove reads mapping to the lambda phage genome from a fastq file. | remove reads mapping, lambda phage genome, fastq file, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/nanolyse/ | SCR_024125 | nanolyse | 2026-02-17 10:04:06 | 5 | ||||||||
|
libncl Resource Report Resource Website |
libncl (RRID:SCR_024080) | software library, software resource, software toolkit | 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. | interpreting data files in NEXUS format, NEXUS Class Library, phylogenetic analyses, interpreting data files written in NEXUS format, | is listed by: Debian | PMID:14630669 | Free, Available for download, Freely available, | OMICS_20523 | https://sources.debian.org/src/libncl/ https://sources.debian.org/src/ncl/ |
SCR_024080 | NCL - the NEXUS Class Library, ncl, NCL | 2026-02-17 10:04:34 | 0 | ||||||
|
libqes Resource Report Resource Website |
libqes (RRID:SCR_024083) | software library, software resource, software toolkit | Software C library with bioinformatic focus optimised for speed and clean API. | C library, focus optimised for speed and clean API, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20524 | https://sources.debian.org/src/libqes/ | SCR_024083 | 2026-02-17 10:04:36 | 0 | ||||||||
|
medicalterms Resource Report Resource Website |
medicalterms (RRID:SCR_024117) | software library, software resource, software toolkit | Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words. | create specialized dictionaries, medical terms, various languages, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/medicalterms/ | SCR_024117 | hunspell-de-med, wgerman-medical | 2026-02-17 10:04:37 | 0 | ||||||||
|
Populations Resource Report Resource Website |
Populations (RRID:SCR_024175) | software library, software resource, software toolkit | 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 | 2026-02-17 10:04:39 | 0 | |||||||
|
quicktree Resource Report Resource Website 10+ mentions |
quicktree (RRID:SCR_024205) | software library, software resource, software toolkit | 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 | 2026-02-17 10:04:40 | 12 | ||||||||
|
pycoqc Resource Report Resource Website 10+ mentions |
pycoqc (RRID:SCR_024185) | software resource, software toolkit | Software application to compute metrics and generate interactive QC plots for Oxford Nanopore technologies sequencing data. | compute metrics, generate interactive QC plots, Oxford Nanopore technologies sequencing data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pycoqc/ | SCR_024185 | 2026-02-17 10:04:38 | 18 | |||||||||
|
python-airr Resource Report Resource Website |
python-airr (RRID:SCR_024187) | software library, software resource, software toolkit | 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 | 2026-02-17 10:04:39 | 0 | |||||||||
|
annotate Resource Report Resource Website |
annotate (RRID:SCR_024221) | software resource, software toolkit | Software R package for using R enviroments for annotation. | R enviroments, annotation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-annotate/ | SCR_024221 | 2026-02-17 10:04:07 | 0 | |||||||||
|
affyio Resource Report Resource Website |
affyio (RRID:SCR_024223) | software library, software resource, software toolkit | 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 | 2026-02-17 10:04:39 | 0 | ||||||||
|
altcdfenvs Resource Report Resource Website |
altcdfenvs (RRID:SCR_024225) | software resource, software toolkit | Software R package contains convenience data structures and functions to handle cdfenvs. | convenience data structures and functions, handle cdfenvs, | is listed by: Debian | PMID:15310390 | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-altcdfenvs/ | SCR_024225 | alternative CDF environments | 2026-02-17 10:04:40 | 0 | |||||||
|
pssh2 Resource Report Resource Website |
pssh2 (RRID:SCR_024181) | software library, software resource, software toolkit | 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 | 2026-02-17 10:04:38 | 0 | |||||||||
|
pyepl Resource Report Resource Website 1+ mentions |
pyepl (RRID:SCR_024182) | software library, software resource, software toolkit | 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 | 2026-02-17 10:04:06 | 3 | ||||||||
|
pbcopper Resource Report Resource Website |
pbcopper (RRID:SCR_024152) | software library, software resource, software toolkit | 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 | 2026-02-17 10:04:37 | 0 | |||||||||
|
Parsnp Resource Report Resource Website 10+ mentions |
Parsnp (RRID:SCR_024153) | software library, software resource, software toolkit | 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 | 2026-02-17 10:04:06 | 39 | ||||||
|
PDB2PQR Resource Report Resource Website 1+ mentions |
PDB2PQR (RRID:SCR_024155) | software library, software resource, software toolkit | 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 | 2026-02-17 10:04:38 | 2 | ||||||
|
PfTools Resource Report Resource Website 1+ mentions |
PfTools (RRID:SCR_024158) | software library, software resource, software toolkit | 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 | 2026-02-17 10:04:38 | 2 |
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