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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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CARD Resource Report Resource Website 100+ mentions |
CARD (RRID:SCR_023995) | data or information resource, database | Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes. | Antibiotic resistance data, resistance genes and associated phenotypes, resistance genes, phenotypes, | is listed by: Debian | PMID:31665441 | Free, Available for download, Freely available | r3d100012727 | https://doi.org/10.17616/R3WN59 | https://sources.debian.org/src/card-rgi/ | SCR_023995 | SciCrunch Registry | card-rgi, Comprehensive Antibiotic Resistance Database, The Comprehensive Antibiotic Resistance Database | 2026-10-24 12:51:59 | 485 | |||||
|
BioCocoa Resource Report Resource Website |
BioCocoa (RRID:SCR_023977) | software application, software resource | Open source framework for bioinformatics written in Objective-C. Provides Cocoa and GNUstep programmers with full suite of APIs for handling and manipulating biological sequences. | APIs for handling and manipulating biological sequences, | is listed by: Debian | Free, Available for download, Freely available | OMICS_19790 | https://sources.debian.org/src/biococoa/ | SCR_023977 | SciCrunch Registry | biococoa | 2026-10-24 12:51:59 | 0 | |||||||
|
Biber Resource Report Resource Website |
Biber (RRID:SCR_023973) | software application, software resource | Software bibliography processing backend for LaTeX biblatex package. Supports unsurpassed feature set for automated conformance to complex bibliography style requirements such as labelling, sorting and name handling. BibTeX replacement for users of BibLaTeX. | bibliography processing backend, LaTeX biblatex package, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/biber/, https://sourceforge.net/projects/biblatex-biber/files/latest/download | SCR_023973 | SciCrunch Registry | biber | 2026-10-24 12:51:59 | 0 | ||||||||
|
CamiTK Resource Report Resource Website |
CamiTK (RRID:SCR_023984) | software application, software resource | Software Computer Assisted Medical Intervention Tool Kit helps researchers and clinicians to easily and rapidly collaborate in order to prototype CAMI applications, that feature medical images, surgical navigation and biomechanical simulations.Open source, cross-platform generic tool, written in C++, which can handle medical images, surgical navigations and biomechanical simulations. | C++, medical images, surgical navigations, biomechanical simulations, | is listed by: Debian | DOI:10.1007/8415_2012_118 | Free, Available for download, Freely available | https://sources.debian.org/src/camitk/ | SCR_023984 | SciCrunch Registry | camitk, Computer Assisted Medical Intervention Tool Kit | 2026-10-24 12:51:59 | 0 | |||||||
|
Aghermann Resource Report Resource Website |
Aghermann (RRID:SCR_023965) | software application, software resource | Sotware tool designed to run Process S simulations on Slow Wave Activity profiles from human EEG recordings.Produces set of sleep homeostat parameters which can be used to describe and differentiate individual sleepers, such as short vs long sleepers, early vs late, etc.Sleep research experiment manager, with facility for reading, displaying, and manual and semi-automatic scoring EEG recordings in edf format; conventional PSD and EEG Microcontinuity profiles; artifact detection; Independent Component Analysis; basic sleep analysis NREM-REM cycle detection. | Sleep research experiment manager, Process S simulations, Slow Wave Activity, human EEG recordings, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/aghermann/ | SCR_023965 | SciCrunch Registry | aghermann | 2026-10-24 12:51:59 | 0 | ||||||||
|
Bio-ASN1-EntrezGene Resource Report Resource Website |
Bio-ASN1-EntrezGene (RRID:SCR_024056) | software application, software resource | Software regular expression based Perl Parser for NCBI Entrez Gene genome databases. Parses ASN.1-formatted Entrez Gene record and returns data structure that contains all data items from gene record. | Perl parser, NCBI Entrez Gene genome databases parser, ASN.1-formatted Entrez Gene record parser, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-asn1-entrezgene-perl/ | SCR_024056 | SciCrunch Registry | libbio-asn1-entrezgene-perl, Bio-ASN1-EntrezGene - Regular expression-based Perl Parser for NCBI Entrez Gene | 2026-10-24 12:51:59 | 0 | ||||||||
|
AcePerl Resource Report Resource Website |
AcePerl (RRID:SCR_024057) | software application, software resource | Software provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously. | software interface, provides interface to ACEDB object-oriented database, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libace-perl/, https://github.com/WormBase/AcePerl | SCR_024057 | SciCrunch Registry | Ace, ACE, libace-perl, Ace-Perl, ace-perl, Ace - Object-Oriented Access to ACEDB Databases | 2026-10-24 12:51:59 | 0 | ||||||||
|
shapeit4 Resource Report Resource Website 10+ mentions |
shapeit4 (RRID:SCR_024335) | software application, software resource | Software tool for estimation of haplotypes aka phasing for SNP array and high coverage sequencing data. The version 4 is refactored and improved version of SHAPEIT algorithm with multiple key additional features. | estimation of haplotypes, phasing, SNP array data, high coverage sequencing data, | is listed by: Debian | PMID:31780650 | Free, Available for download, Freely available, | https://sources.debian.org/src/shapeit4/ | SCR_024335 | SciCrunch Registry | SHAPEIT, SHAPEIT4 | 2026-10-24 12:52:00 | 23 | |||||||
|
sailfish Resource Report Resource Website 1+ mentions |
sailfish (RRID:SCR_024326) | software application, software resource | Software tool that implements novel, alignment free algorithm for estimation of isoform abundances directly from set of reference sequences and RNA-seq reads. | estimation of isoform abundances, reference sequences, RNA-seq reads, | is listed by: Debian | PMID:24752080 | Free, Available for download, Freely available, | OMICS_03939 | https://sources.debian.org/src/sailfish/ | SCR_024326 | SciCrunch Registry | 2026-10-24 12:51:59 | 1 | |||||||
|
ragout Resource Report Resource Website 1+ mentions |
ragout (RRID:SCR_024206) | software application, software resource | Software tool for chromosome level scaffolding using multiple references. Given initial assembly fragments and one or multiple related references it produces chromosome scale assembly. | chromosome level scaffolding, multiple references, produce chromosome scale assembly, | is listed by: Debian | PMID:30341161 | Free, Available for download, Freely available, | OMICS_07883 | SCR_024206 | SciCrunch Registry | Reference-Assisted Genome Ordering UTility | 2026-10-24 12:51:59 | 1 | |||||||
|
Bio-SamTools Resource Report Resource Website 1+ mentions |
Bio-SamTools (RRID:SCR_024066) | software application, software resource | Software Perl interface to SamTools library for DNA sequencing. | Perl interface, SamTools library, DNA sequencing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-samtools-perl/ | SCR_024066 | SciCrunch Registry | libbio-samtools-perl | 2026-10-24 12:51:59 | 5 | ||||||||
|
skesa Resource Report Resource Website 10+ mentions |
skesa (RRID:SCR_024341) | software application, software resource | Software de-novo sequence read assembler for microbial genomes.Designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.SKESA contigs could be connected into GFA graph using GFA connector. | de-novo sequence read assembler, microbial genomes, create breaks at repeat regions in genome, | is listed by: Debian | PMID:30286803 | Free, Available for download, Freely available, | https://sources.debian.org/src/skesa/ | SCR_024341 | SciCrunch Registry | SKESA | 2026-10-24 12:52:00 | 15 | |||||||
|
sistr Resource Report Resource Website 10+ mentions |
sistr (RRID:SCR_024342) | SISTR | software application, software resource | SISTR command-line tool. Open web accessible tool for rapidly typing and subtyping draft salmonella genome assemblies. | rapidly typing and subtyping draft salmonella genome assemblies, salmonella genome assemblies, | is listed by: Debian | PMID:26800248 | Free, Available for download, Freely available, | OMICS_12011 | https://sources.debian.org/src/sistr/ | SCR_024342 | SciCrunch Registry | Salmonella In Silico Typing Resource | 2026-10-24 12:52:00 | 33 | |||||
|
Bio-SCF Resource Report Resource Website |
Bio-SCF (RRID:SCR_024068) | software application, software resource | Software Perl extension for reading and writting SCF sequence files.This module provides Perl interface to SCF DNA sequencing files. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back. | Perl, Perl extension, reading and writting SCF sequence files, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-scf-perl/ | SCR_024068 | SciCrunch Registry | Bio-SCF - Perl extension for reading and writting SCF sequence files, libbio-scf-perl | 2026-10-24 12:51:59 | 0 | ||||||||
|
pufferfish Resource Report Resource Website |
pufferfish (RRID:SCR_024184) | software application, software resource | Software tool implementing novel indexing data structure for compacted de Bruijn graph and colored compacted de Bruijn graph. | indexing data structure, compacted de Bruijn graph, colored compacted de Bruijn graph, | is listed by: Debian | PMID:29949982 | Free, Available for download, Freely available, | https://sources.debian.org/src/pufferfish/ | SCR_024184 | SciCrunch Registry | 2026-10-24 12:51:59 | 0 | ||||||||
|
rtax Resource Report Resource Website |
rtax (RRID:SCR_024320) | software application, software resource | Software tool for rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene. | taxonomic classification, short paired-end sequence reads, 16S ribosomal RNA gene, | is listed by: Debian | PMID:22237546 | Free, Available for download, Freely available, | OMICS_28979 | https://sources.debian.org/src/rtax/ | SCR_024320 | SciCrunch Registry | 2026-10-24 12:51:59 | 0 | |||||||
|
runcircos-gui Resource Report Resource Website |
runcircos-gui (RRID:SCR_024321) | software application, software resource | GUI tool to run circos | run circos, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/runcircos-gui/ | SCR_024321 | SciCrunch Registry | 2026-10-24 12:51:59 | 0 | |||||||||
|
raccoon Resource Report Resource Website 1+ mentions |
raccoon (RRID:SCR_024201) | software application, software resource | Software graphical interface for preparing AutoDock virtual screenings.Automates some of the most common operations performed when preparing virtual screening. | preparing AutoDock virtual screenings, automates operations for preparing virtual screening, | is listed by: Debian | PMID:21532931 | Free, Available for download, Freely available, | OMICS_21300 | https://sources.debian.org/src/raccoon/ | SCR_024201 | SciCrunch Registry | 2026-10-24 12:51:59 | 1 | |||||||
|
roguenarok Resource Report Resource Website |
roguenarok (RRID:SCR_024316) | software application, software resource | Software tool as versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index. | rogue taxon identification algorithm, maximum agreement subtree, leaf stability index, taxonomic instability index, | is listed by: Debian | PMID:22962004 | Free, Available for download, Freely available, | https://sources.debian.org/src/roguenarok/ | SCR_024316 | SciCrunch Registry | 2026-10-24 12:51:59 | 0 | ||||||||
|
roadtrips Resource Report Resource Website |
roadtrips (RRID:SCR_024318) | software application, software resource | Software C program that performs single SNP, case control association testing in samples with partially or completely unknown population and pedigree structure. | single SNP, case control association testing, testing samples, partially or completely unknown population, pedigree structure, | is listed by: Debian | PMID:20137780 | Free, Available for download, Freely available, | OMICS_21698 | https://sources.debian.org/src/roadtrips/ | SCR_024318 | SciCrunch Registry | ROADTRIPS 2.0 | 2026-10-24 12:51:59 | 0 |
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