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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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pFind Studio: pLink Resource Report Resource Website 10+ mentions |
pFind Studio: pLink (RRID:SCR_000084) | pLink | software resource | Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mass spectrometry, proteomics, pFind Studio, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:22772728 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02404, biotools:pLink-2 | https://github.com/pFindStudio/pLink3/releases | http://pfind.ict.ac.cn/software/pLink/index.html | SCR_000084 | SciCrunch Registry | , pLink, pLink (pFind Studio), pLink2 | 2026-11-07 11:53:52 | 15 | ||||
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Spotfinder Resource Report Resource Website 1+ mentions |
Spotfinder (RRID:SCR_000085) | Spotfinder | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression. | c++ |
is listed by: OMICtools has parent organization: Dana-Farber Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00848 | SCR_000085 | SciCrunch Registry | TIGR Spotfinder | 2026-11-07 11:53:53 | 8 | |||||||
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Parallel-META Resource Report Resource Website 1+ mentions |
Parallel-META (RRID:SCR_000121) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis. | data mining, microbial community data, comparative taxonomics, metagenomic analysis, parallel algorithms | is listed by: OMICtools | PMID:23046922 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01519 | SCR_000121 | SciCrunch Registry | Parallel META, Parallel Meta | 2026-11-07 11:53:53 | 4 | |||||||
|
BioLemmatizer Resource Report Resource Website 1+ mentions |
BioLemmatizer (RRID:SCR_000117) | software resource | A domain-specific lemmatization software tool for the morphological analysis of biomedical literature. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22464129 | Free, Available for download, Freely available | OMICS_04827 | https://sourceforge.net/projects/biolemmatizer/ | SCR_000117 | SciCrunch Registry | 2026-11-07 11:53:53 | 2 | |||||||
|
Orphelia Resource Report Resource Website 1+ mentions |
Orphelia (RRID:SCR_000119) | simulation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A metagenomic open reading frame (ORF) finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin. The resource is based on a two-stage machine learning approach that uses linear discriminants to extract features from the ORFs. An artificial neural network then combines the features and computes a gene probability for each ORF fragment. | metagenomic open reading frame, tool, resource, protein, genes, DNA, phyologenetic origin, machine learning, linear discriminates, artificial neural network, computation, scientific computing, fragment | is listed by: OMICtools | PMID:19429689 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01492 | SCR_000119 | SciCrunch Registry | 2026-11-07 11:53:53 | 2 | ||||||||
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ReQON Resource Report Resource Website |
ReQON (RRID:SCR_000075) | ReQON | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format. | preprocessing, quality control, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22946927 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02033 | SCR_000075 | SciCrunch Registry | Recalibrating Quality Of Nucleotides | 2026-11-07 11:53:51 | 0 | ||||||
|
QuadGT Resource Report Resource Website 1+ mentions |
QuadGT (RRID:SCR_000073) | QuadGT | software resource | Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples. | single-nucleotide variant, sequenced genome, genotype, genome |
is listed by: OMICtools has parent organization: University of Montreal; Quebec; Canada |
Normal, Tumor, Cancer | Canada National Sciences and Engineering Research Council ; Canadian Institutes for Health Research ; Terry Fox Research Institute |
PMID:23734724 | Free, Available for download, Freely available | OMICS_02108 | SCR_000073 | SciCrunch Registry | 2026-11-07 11:53:52 | 1 | |||||
|
SOAPfuse Resource Report Resource Website 1+ mentions |
SOAPfuse (RRID:SCR_000078) | SOAPfuse | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences . | software, resource, open license, DNA sequencing, genome, transcripts, RNA, oligonucleotide |
is listed by: OMICtools is listed by: SourceForge is listed by: SOAP |
PMID:23409703 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01357 | SCR_000078 | SciCrunch Registry | 2026-11-07 11:53:52 | 7 | |||||||
|
Treephyler Resource Report Resource Website 1+ mentions |
Treephyler (RRID:SCR_000109) | Treephyler | software resource | A software tool for fast taxonomic profiling of metagenomes. | metagenome, perl, nucleotide, protein, next-generation sequencing | is listed by: OMICtools | PMID:20172941 | Free, Available for download, Freely available | OMICS_01469 | SCR_000109 | SciCrunch Registry | Treephyler: fast taxonomic profiling of metagenomes | 2026-11-07 11:53:54 | 1 | ||||||
|
FastQ Screen Resource Report Resource Website 50+ mentions |
FastQ Screen (RRID:SCR_000141) | FastQ Screen | software resource | Software that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. | perl, FASEB list |
is listed by: OMICtools has parent organization: Babraham Institute |
PMID:30254741 | Free, Available for download, Freely available | OMICS_01042 | SCR_000141 | SciCrunch Registry | 2026-11-07 11:53:54 | 50 | |||||||
|
GenomicRanges Resource Report Resource Website 50+ mentions |
GenomicRanges (RRID:SCR_000025) | GenomicRanges | software resource | Software package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. | genomic interval |
is used by: riboWaltz is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | SCR_018096, OMICS_01161 | SCR_000025 | SciCrunch Registry | GenomicRanges - Representation and manipulation of genomic intervals | 2026-11-07 11:53:50 | 56 | |||||||
|
GEOquery Resource Report Resource Website 10+ mentions |
GEOquery (RRID:SCR_000146) | GEOquery | software resource | Software that establishes a bridge between GEO and BioConductor. | microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Expression Omnibus is related to: GEO2R has parent organization: Bioconductor has parent organization: National Institutes of Health |
PMID:17496320 | Free, Available for download, Freely available | biotools:geoquery, OMICS_01972 | https://bio.tools/geoquery, https://sources.debian.org/src/r-bioc-geoquery/ | SCR_000146 | SciCrunch Registry | GEOquery - Get data from NCBI Gene Expression Omnibus (GEO) | 2026-11-07 11:53:53 | 20 | |||||
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JChemPaint Resource Report Resource Website 1+ mentions |
JChemPaint (RRID:SCR_000095) | JCP | software resource | Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK). | applet, mac os x, unix/linux, windows, java | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_04959 | https://github.com/JChemPaint/jchempaint | SCR_000095 | SciCrunch Registry | 2026-11-07 11:53:52 | 1 | |||||||
|
BSmooth-align Resource Report Resource Website 1+ mentions |
BSmooth-align (RRID:SCR_000013) | alignment software, data analysis software, data processing software, image analysis software, software application, software resource | Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements. | bisulfite sequence, read-level methylation, bisulfite sequence reads alignment, | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01846 | SCR_000013 | SciCrunch Registry | 2026-11-07 11:53:50 | 1 | |||||||||
|
Sequence Read Format Resource Report Resource Website 1+ mentions |
Sequence Read Format (RRID:SCR_000132) | SRF | data or information resource, interchange format, narrative resource, standard specification | A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology. | dna sequence, dna sequencing, interchange format |
is listed by: OMICtools has parent organization: SourceForge |
Public, A C++ implementation of Sequence Read Format is available | OMICS_05130 | SCR_000132 | SciCrunch Registry | Sequence Read Format (SRF) | 2026-11-07 11:53:54 | 1 | |||||||
|
DOCK Resource Report Resource Website 10+ mentions |
DOCK (RRID:SCR_000128) | DOCK | software resource | An algorithm used to predict and analyse binding modes of docking molecules. Users can search ligand databases for compounds that inhibit enzymatic activity and bind to particular molecules and nucleic acid targets. Molecular docking is used to predict a predominant binding mode(s) of a ligand in three-dimensional structure. This method can be used for molecular biology and computer-assisted drug design. | molecule docking, ligand model, drug design, molecular biology |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
Available to the research community, Free for the academic community, License fee for industrial organizations, Available for download | OMICS_01598 | SCR_000128 | SciCrunch Registry | UCSF DOCK | 2026-11-07 11:53:54 | 16 | |||||||
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exomeSuite Resource Report Resource Website |
exomeSuite (RRID:SCR_000129) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease. | standalone software, c, matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24603341 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04839 | SCR_000129 | SciCrunch Registry | 2026-11-07 11:53:53 | 0 | ||||||||
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RmiR.Hs.miRNA Resource Report Resource Website |
RmiR.Hs.miRNA (RRID:SCR_000101) | software resource | Software package for various databases of microRNA Targets. | software package, unix/linux, mac os x, windows, r, annotation data, custom db schema, mirna |
is listed by: OMICtools is related to: CRAN has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05797 | SCR_000101 | SciCrunch Registry | RmiR.Hs.miRNA: Various databases of microRNA Targets | 2026-11-07 11:53:52 | 0 | ||||||||
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nFuse Resource Report Resource Website 1+ mentions |
nFuse (RRID:SCR_000066) | nFuse | software resource | Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS). | cancer, genomics |
is listed by: OMICtools is listed by: Google Code has parent organization: Simon Fraser University; British Columbia; Canada |
Cancer | PMID:22745232 | Free, Available for download, Freely available, | OMICS_01353 | SCR_000066 | SciCrunch Registry | nFuse: Discovery of Complex Genomic Rearrangements in Cancer | 2026-11-07 11:53:51 | 2 | |||||
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GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | data analysis software, data processing software, software application, software resource | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
ADVANCE Program at Brown University ; Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/, https://bio.tools/gasv | SCR_000061 | SciCrunch Registry | Geometric Analysis of Structural Variants | 2026-11-07 11:53:51 | 4 |
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