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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software application, software resource | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM071558; NIDDK R01 DK088541; NLM RC2 LM010994; NIDDK P01 DK056492; NIDDK RC4DK090860; NCRR KL2 RR029885 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-08-04 09:43:52 | 4 | ||||
|
ABACAS Resource Report Resource Website 100+ mentions |
ABACAS (RRID:SCR_015852) | ABACAS | software application, software resource | Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account. | contiguation, primer, shotgun assembled contig, reference sequence, assembled sequence |
is listed by: Debian is listed by: OMICtools |
European Union LSHP-LT-2004-503578; Wellcome Trust Sanger Institute |
Free, Available for download | OMICS_06933 | https://sourceforge.net/projects/abacas/files/, https://sources.debian.org/src/abacas/ | SCR_015852 | ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences, Algorithm Based Automatic Contiguation of Assembled Sequences (ABACAS), Algorithm Based Automatic Contiguation of Assembled Sequences | 2026-08-04 09:43:45 | 174 | |||||
|
DOMAINATRIX Resource Report Resource Website |
DOMAINATRIX (RRID:SCR_016084) | software application, software resource | Software for protein domain search. It is a part of Embassy software package. | protein, domain, search, molecular, biology | is listed by: Debian | Free, Available for download, Freely available | http://emboss.sourceforge.net/what/, https://sources.debian.org/src/embassy-domainatrix/ | SCR_016084 | Embassy-domainatrix | 2026-08-04 09:43:48 | 0 | ||||||||
|
Ecopcr Resource Report Resource Website 10+ mentions |
Ecopcr (RRID:SCR_016082) | Ecopcr | software application, software resource | Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | electronic, PCR, estimate, primers, quality, barcode |
is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_19861 | https://sources.debian.org/src/ecopcr/ | http://www.grenoble.prabi.fr/trac/ecoPCR/ | SCR_016082 | Ecopcr: Electronic polymerase chain reaction | 2026-08-04 09:43:49 | 27 | |||||
|
Clinotator Resource Report Resource Website 1+ mentions |
Clinotator (RRID:SCR_016054) | software application, software resource | Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics. | clinical, age, weight, score, metric, vcf, python, nbci, annotation, variant, scoring, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free | biotools:clinotator | https://bio.tools/clinotator | SCR_016054 | clinotator.py | 2026-08-04 09:43:47 | 2 | |||||||
|
QGIS Resource Report Resource Website 100+ mentions |
QGIS (RRID:SCR_018507) | software application, software resource | Open source cross platform desktop geographic information system application that supports viewing, editing, and analysis of geospatial data. Functions as geographic information system software, allowing users to analyze and edit spatial information, in addition to composing and exporting graphical maps. | Geographic information system, viewing, editing, analysis, geospatial data, spatial information analysis, graphical map, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:QGIS | https://bio.tools/QGIS | SCR_018507 | 2026-08-04 09:44:21 | 400 | ||||||||
|
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 | libbio-asn1-entrezgene-perl, Bio-ASN1-EntrezGene - Regular expression-based Perl Parser for NCBI Entrez Gene | 2026-08-04 09:45:24 | 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 | Ace, ACE, libace-perl, Ace-Perl, ace-perl, Ace - Object-Oriented Access to ACEDB Databases | 2026-08-04 09:45:24 | 0 | ||||||||
|
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 | libbio-samtools-perl | 2026-08-04 09:45:24 | 5 | ||||||||
|
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 | Bio-SCF - Perl extension for reading and writting SCF sequence files, libbio-scf-perl | 2026-08-04 09:45:25 | 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 | 2026-08-04 09:45:28 | 0 | ||||||||
|
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 | biococoa | 2026-08-04 09:45:23 | 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 | biber | 2026-08-04 09:45:23 | 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 | camitk, Computer Assisted Medical Intervention Tool Kit | 2026-08-04 09:45:23 | 0 | |||||||
|
SeqLib Resource Report Resource Website 1+ mentions |
SeqLib (RRID:SCR_024091) | software application, software resource | Software C++ htslib/bwa-mem/fermi interface for interrogating sequence data | interrogating sequence data, | is listed by: Debian | DOI:10.1093/bioinformatics/btw741 | Free, Available for download, Freely available, | OMICS_14682 | https://sources.debian.org/src/libseqlib/ | SCR_024091 | libseqlib | 2026-08-04 09:45:24 | 1 | ||||||
|
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 | aghermann | 2026-08-04 09:45:23 | 0 | ||||||||
|
MacSyFinder Resource Report Resource Website 10+ mentions |
MacSyFinder (RRID:SCR_024106) | software application, software resource | Software tool to mine genomes for molecular systems with Application to CRISPR-Cas Systems. Detection of macromolecular systems in protein datasets using systems modelling and similarity search. | Detection of macromolecular system, protein datasets, mine genomes, molecular systems, | is listed by: Debian | PMID:25330359 | Free, Available for download, Freely available, | OMICS_20116 | https://sources.debian.org/src/macsyfinder/ | SCR_024106 | macsyfinder | 2026-08-04 09:45:25 | 22 | ||||||
|
Nanocall Resource Report Resource Website |
Nanocall (RRID:SCR_024124) | software application, software resource | Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller. | basecaller, Oxford Nanopore Technologies, sequencing data, | is listed by: Debian | PMID:27614348 | Free, Available for download, Freely available, | OMICS_11495 | https://sources.debian.org/src/nanocall/ | SCR_024124 | Nanocall, nanocall | 2026-08-04 09:45:25 | 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 | SHAPEIT, SHAPEIT4 | 2026-08-04 09:45:30 | 21 | |||||||
|
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 | 2026-08-04 09:45:29 | 1 |
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