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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-07-26 09:08:17 | 0 | |||||||
|
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 | 2026-07-26 09:08:19 | 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 | ROADTRIPS 2.0 | 2026-07-26 09:08:23 | 0 | ||||||
|
vcfanno Resource Report Resource Website |
vcfanno (RRID:SCR_024372) | software application, software resource | Software tool for flexible annotation of genetic variants.Extracts and summarizes attributes from multiple annotation files and integrates annotations within INFO column of the original VCF file. | annotation of genetic variants, extracts and summarizes attributes, multiple annotation files, integrates annotations, VCF file, | is listed by: Debian | PMID:27250555 | Free, Available for download, Freely available, | OMICS_11863 | https://sources.debian.org/src/vcfanno/ | SCR_024372 | 2026-07-26 09:08:24 | 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 | 2026-07-26 09:08:19 | 1 | ||||||
|
VirulenceFinder Resource Report Resource Website 100+ mentions |
VirulenceFinder (RRID:SCR_024371) | software application, software resource | Software tool for detection of E. coli virulence genes. Used to identify viruelnce genes in total or partial sequenced isolates of bacteria. E. coli, Enterococcus, S. aureus and Listeria are available.for detection of E. coli virulence genes. | detection of E. coli virulence genes, | is listed by: Debian | PMID:24574290 | Free, Available for download, Freely available, | OMICS_17862 | https://sources.debian.org/src/virulencefinder/ | SCR_024371 | virulencefinder | 2026-07-26 09:08:25 | 262 | ||||||
|
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 | 2026-07-26 09:08:16 | 0 | ||||||||
|
strap-base Resource Report Resource Website |
strap-base (RRID:SCR_024351) | software application, software resource | Software tool as Intuitive Editor for annotated multiple Sequence and Structure Alignments. | editor for annotated multiple Sequence and Structure Alignments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/strap-base/ | SCR_024351 | 2026-07-26 09:08:20 | 0 | |||||||||
|
qcat Resource Report Resource Website 10+ mentions |
qcat (RRID:SCR_024195) | software application, software resource | Software Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files. | command-line tool, demultiplexing Oxford Nanopore reads, reads from FASTQ files, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/qcat/ | SCR_024195 | 2026-07-26 09:08:23 | 12 | |||||||||
|
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 | 2026-07-26 09:08:20 | 22 | ||||||
|
tiddit Resource Report Resource Website 1+ mentions |
tiddit (RRID:SCR_024361) | software application, software resource | Software tool as structural variant calling. | structural variant calling, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/tiddit/ | SCR_024361 | TIDDIT | 2026-07-26 09:08:24 | 3 | ||||||||
|
Yanagiba Resource Report Resource Website |
Yanagiba (RRID:SCR_024362) | software application, software resource | Software tool to filter and slice Nanopore reads which have been basecalled with Albacore. | filter and slice Nanopore reads, basecalled with Albacore, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/yanagiba/ | SCR_024362 | yanagiba | 2026-07-26 09:08:20 | 0 | ||||||||
|
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 | 2026-07-26 09:08:20 | 0 | ||||||
|
swarm Resource Report Resource Website 1+ mentions |
swarm (RRID:SCR_024358) | software application, software resource | Software tool as clustering method for amplicon-based studies. | clustering method, amplicon based studies, | is listed by: Debian | PMID:26713226 | Free, Available for download, Freely available, | OMICS_14578 | https://sources.debian.org/src/swarm/ | SCR_024358 | 2026-07-26 09:08:25 | 4 | |||||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software application, software resource | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-07-26 09:02:49 | 0 | ||||||
|
FLOSS Resource Report Resource Website |
FLOSS (RRID:SCR_000836) | FLOSS | software application, software resource | Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:floss, nlx_154319 | https://bio.tools/floss | SCR_000836 | FLexible Ordered SubSet analysis | 2026-07-26 09:02:53 | 0 | |||||||
|
DINDEL Resource Report Resource Website 10+ mentions |
DINDEL (RRID:SCR_001827) | Dindel | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems). | indel, short-read, next generation sequence, illumina, gene, genetic, genomic, c++, linux, macos, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:20980555 DOI:10.1101/gr.112326.110 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154283, OMICS_00096, biotools:dindel | https://bio.tools/dindel, https://sources.debian.org/src/dindel/ | http://www.sanger.ac.uk/resources/software/dindel/ | SCR_001827 | Dindel: Accurate indel calls from short-read data | 2026-07-26 09:03:10 | 44 | ||||
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PEDIGRAPH Resource Report Resource Website 10+ mentions |
PEDIGRAPH (RRID:SCR_001938) | Pedigraph | software application, software resource | A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles | gene, genetic, genomic, c, c++, ms-windows, linux, pedigree, java, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:14986440 | Acknowledgement required, Copyrighted | biotools:pedigraph, OMICS_00212, nlx_154519 | https://bio.tools/pedigraph | SCR_001938 | 2026-07-26 09:03:07 | 17 | ||||||
|
Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software application, software resource | A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo, https://sources.debian.org/src/aragorn/ | SCR_001936 | 2026-07-26 09:03:11 | 274 | ||||||
|
PsychoPy Resource Report Resource Website 1000+ mentions |
PsychoPy (RRID:SCR_006571) | PsychoPy | software application, software resource | Open source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It is intended as a free, powerful alternative to Presentation or e-Prime. | console (text based), experimental control, freebsd, linux, macos, microsoft, magnetic resonance, posix/unix-like, python, win32 (ms windows), windows, neuroscience, psychology, psychophysics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: University of Nottingham; Nottingham; United Kingdom |
PMID:17254636 PMID:19198666 |
GNU General Public License | nlx_155928 | http://www.nitrc.org/projects/psychopy, https://sources.debian.org/src/psychopy/ | SCR_006571 | PsychoPy - Psychology software in Python | 2026-07-26 09:04:19 | 1975 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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