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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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In-Silico PCR Resource Report Resource Website 10+ mentions |
In-Silico PCR (RRID:SCR_003089) | In-Silico PCR | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool that searches a sequence database with a pair of PCR primers, using an indexing strategy for fast performance. When successful, the search returns a sequence output file in fasta format containing all sequence in the database that lie between and include the primer pair. The fasta header describes the region in the database and the primers. The fasta body is capitalized in areas where the primer sequence matches the database sequence and in lower-case elsewhere. Sources and executables to run batch jobs on your own server are available free for academic, personal, and non-profit purposes. Non-exclusive commercial licenses are also available. | pcr primer, polymerase chain reaction, primer |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
Free, Available for download, Freely available | OMICS_02344 | SCR_003089 | SciCrunch Registry | UCSC In-Silico PCR | 2026-10-10 12:36:46 | 17 | |||||||
|
HYDEN Resource Report Resource Website 10+ mentions |
HYDEN (RRID:SCR_003126) | HYDEN | software resource | Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request). | degenerate, primer, dna sequence, primer design, degenerate primer, windows, linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Tel Aviv University; Ramat Aviv; Israel |
PMID:17951798 | Free, Available for download, Freely available | OMICS_02338, biotools:hyden | https://bio.tools/hyden | SCR_003126 | SciCrunch Registry | HYDEN - A Software for Designing Degenerate Primers, HighlY DEgeNerate primers | 2026-10-10 12:36:47 | 12 | |||||
|
MISO Resource Report Resource Website 100+ mentions |
MISO (RRID:SCR_003124) | data analysis software, data processing software, sequence analysis software, software application, software resource | Probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq and identifies differentially regulated isoforms or exons across samples. | probabilistic framework, framework, bayesian inference, isoform |
is listed by: OMICtools is related to: Sashimiplot has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
DOI:10.1038/nmeth.1528 | Free, Available for download, Freely available | OMICS_01337 | https://github.com/yarden/MISO | SCR_003124 | SciCrunch Registry | Mixture of Isoforms (MISO), Mixture of Isoforms | 2026-10-10 12:36:33 | 181 | ||||||
|
bwtool Resource Report Resource Website 10+ mentions |
bwtool (RRID:SCR_003035) | software resource | A command-line utility for bigWig files designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Its functionality is subdivided into subprograms that roughly fall into three categories: data extraction, analysis, and data modification, although e.g. in the case of the matrix program or the sax program, the boundary between data extraction and analysis isn't very strong. The data modification programs all have the behavior that a bigWig is inputted and a new bigWig is outputted. | standalone software, unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:2448936 | Free, Available for download, Freely available | biotools:bwtool, OMICS_05125 | https://bio.tools/bwtool | SCR_003035 | SciCrunch Registry | 2026-10-10 12:36:20 | 22 | |||||||
|
enviPat Resource Report Resource Website 10+ mentions |
enviPat (RRID:SCR_003034) | software resource | Software for fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Freely available | OMICS_02408 | SCR_003034 | SciCrunch Registry | enviPat: Isotope pattern profile and centroid calculation for mass spectrometry | 2026-10-10 12:36:46 | 33 | ||||||||
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MoSDi Resource Report Resource Website 1+ mentions |
MoSDi (RRID:SCR_003037) | data analysis software, data processing software, software application, software resource, software toolkit | Sequence analysis toolkit that contains a lot of sequence analysis algorithms, including methods for 1) motif statistics, e.g. compute the exact occurrence count distribution of a motif, 2) exact motif discovery: extraction of motifs with provably optimal p-value, 3) analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text, 4) statistics of fragment masses resulting from proteolytic cleavage of proteins, 5) computing the expectated read length of sequencing reads for a given dispensation order (for 454 or IonTorrent) and 6) analysing sensitivity of spaced alignment seeds. | standalone software, unix/linux, motif |
is listed by: OMICtools has parent organization: Google Code |
PMID:19478010 | Free, Freely available | OMICS_06271 | https://bio.tools/mosdi | SCR_003037 | SciCrunch Registry | Motif Statistics and Discovery, Motif Statistics and Discovery - Sequence analysis toolkit for bioinformatics | 2026-10-10 12:36:30 | 2 | ||||||
|
JASPAR Resource Report Resource Website 5000+ mentions |
JASPAR (RRID:SCR_003030) | JASPAR | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. | structural class, transcription factor binding site, profile, regulatory region, genome, genomic, matrix, transcription factor, binding site, dna, FASEB list |
is listed by: OMICtools is listed by: re3data.org is related to: Babelomics has parent organization: University of Copenhagen; Copenhagen; Denmark has parent organization: Karolinska Institute; Stockholm; Sweden |
Carlsberg Foundation ; EMBRACEa Sixth Framework Network of Excellence ; European Union ; Novo Nordisk Foundation ; Sars Centre |
PMID:18006571 PMID:16381983 PMID:14681366 |
Free, Freely available | r3d100010091, OMICS_00538, nif-0000-03061 | https://doi.org/10.17616/R3QC7R | http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl, http://jaspar.cgb.ki.se | SCR_003030 | SciCrunch Registry | JASPAR, JASPAR CORE, JASPAR CORE database, JASPAR database | 2026-10-10 12:36:21 | 5785 | |||
|
SMRT View Resource Report Resource Website 1+ mentions |
SMRT View (RRID:SCR_003029) | software resource | An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results. | standalone software, unix/linux, mac os x, windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:smrt_view, OMICS_05137 | https://bio.tools/smrt_view | SCR_003029 | SciCrunch Registry | SMRT-View | 2026-10-10 12:36:20 | 9 | |||||||
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pbh5tools Resource Report Resource Website 10+ mentions |
pbh5tools (RRID:SCR_003027) | software resource | Software tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from cmp.h5 and bas.h5 files. | standalone software | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_05138 | http://132.248.34.22:8080/smrtanalysis/doc/bioinformatics-tools/pbh5tools/doc/index.html | SCR_003027 | SciCrunch Registry | 2026-10-10 12:36:46 | 10 | ||||||||
|
DiNuP Resource Report Resource Website |
DiNuP (RRID:SCR_003046) | data analysis software, data processing software, software application, software resource | Software that compares the nucleosome profiles generated by high-throughput sequencing between different conditions. It provides a statistical p-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the FDR as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise. | nucleosome profile, regions of differential nucleosome positioning |
is listed by: OMICtools has parent organization: Tongji University; Shanghai; China |
PMID:22668788 | Free, Freely available | OMICS_00503 | SCR_003046 | SciCrunch Registry | DiNuP - A Systematic Approach to Identify Regions of Differential Nucleosome Positioning | 2026-10-10 12:36:20 | 0 | |||||||
|
ProRata Resource Report Resource Website 1+ mentions |
ProRata (RRID:SCR_002988) | software resource | A quantitative proteomics software program for accurate protein abundance ratio estimation with confidence interval evaluation. | standalone software, mass spectrometry, proteomics, stable isotope labeling, quantitative proteomics, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:17037911 | GNU General Public License, v3 | biotools:prorata, OMICS_02502 | https://bio.tools/prorata | SCR_002988 | SciCrunch Registry | ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation, prorata - Quantitative Proteomics Software | 2026-10-10 12:36:20 | 9 | ||||||
|
BioPerl Resource Report Resource Website 100+ mentions |
BioPerl (RRID:SCR_002989) | BioPerl | data or information resource, narrative resource, software repository, software resource, software toolkit, source code, wiki | BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, biology, ontology, library, sequence, analysis, computational, application, pipeline, bioinformatics, sequence, annotation, module, life science, python, java, genome, software library, parse, manipulate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Gene Ontology is related to: OBO has parent organization: Duke University; North Carolina; USA has parent organization: European Bioinformatics Institute is required by: RelocaTE |
NIGMS T32 GM07754-22; NHGRI K22 HG00056; NHGRI K22 HG-00064-01; NHGRI HG00739; NHGRI P41HG02223 |
PMID:12368254 DOI:10.1101/gr.361602 |
Free, Available for download, Freely available | OMICS_04849, nif-0000-30188, biotools:bioperl | https://bio.tools/bioperl, https://sources.debian.org/src/bioperl/ | SCR_002989 | SciCrunch Registry | 2026-10-10 12:36:29 | 408 | |||||
|
Gene Set Enrichment Analysis Resource Report Resource Website 10000+ mentions |
Gene Set Enrichment Analysis (RRID:SCR_003199) | GSEA | data analysis software, data processing software, software application, software resource, software toolkit | Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes. | gene, expression, profile, pathway, data, set, phenotype, genome, enrichment, RNA, analysis, bio.tools, bio.tools |
is used by: Molecular Signatures Database is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GoMapMan has parent organization: Broad Institute |
NCI ; NIGMS ; NIH |
PMID:16199517 | Free, Freely available | SCR_016882, nif-0000-30629, biotools:gsea, OMICS_02279 | http://www.broad.mit.edu/gsea, https://bio.tools/gsea | SCR_003199 | SciCrunch Registry | GSEA, Gene Set Enrichment Analysis, Gene Set Enrichment Analysis (GSEA) | 2026-10-10 12:36:47 | 20985 | ||||
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r3Cseq Resource Report Resource Website 10+ mentions |
r3Cseq (RRID:SCR_003198) | r3Cseq | data analysis software, data processing software, software application, software resource | An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results. | next-generation sequencing, genomic, interaction, chromosome conformation capture, chromosome, 3c-seq, r |
is listed by: OMICtools has parent organization: University of Bergen; Bergen; Norway has parent organization: Bioconductor |
PMID:23671339 | Free, Freely available | OMICS_01560 | SCR_003198 | SciCrunch Registry | 2026-10-10 12:36:35 | 24 | |||||||
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Stacks Resource Report Resource Website 500+ mentions |
Stacks (RRID:SCR_003184) | Stacks | data analysis software, data processing software, software application, software resource | A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. | population genomics, genetic map, phylogenetics, genetics, next-generation sequencing, rad-seq, genotype-by-sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Oregon; Oregon; USA |
PMID:23701397 PMID:22384329 DOI:10.1111/mec.12354 |
Free, Available for download, Freely available | OMICS_01567, biotools:stacks | https://bio.tools/stacks, https://sources.debian.org/src/stacks/ | SCR_003184 | SciCrunch Registry | 2026-10-10 12:36:35 | 671 | ||||||
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RNAhybrid Resource Report Resource Website 500+ mentions |
RNAhybrid (RRID:SCR_003252) | RNAhybrid | analysis service resource, data analysis service, production service resource, service resource, software resource | Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction. | microrna, target prediction, free energy, rna, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15383676 DOI:10.1261/rna.5248604 |
Free, Available for download, Freely available | OMICS_00416, biotools:rnahybrid, nif-0000-31412 | https://bio.tools/rnahybrid, https://sources.debian.org/src/rnahybrid/ | SCR_003252 | SciCrunch Registry | 2026-10-10 12:36:25 | 517 | ||||||
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PlantLoc Resource Report Resource Website 1+ mentions |
PlantLoc (RRID:SCR_003138) | PlantLoc | analysis service resource, data analysis service, production service resource, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif. | subcellular localization, protein |
is listed by: OMICtools has parent organization: Tongji University; Shanghai; China |
PMID:23729470 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01632 | SCR_003138 | SciCrunch Registry | PlantLoc: Plant Proteins Subcellular Localization Prediction Server | 2026-10-10 12:36:23 | 4 | ||||||
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Assembly Based ReAligner Resource Report Resource Website 10+ mentions |
Assembly Based ReAligner (RRID:SCR_003277) | ABRA | software resource | Software that is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular). | standalone software, c, c++, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24907369 | Free, Available for download, Freely available | OMICS_04668, biotools:abra | https://bio.tools/abra | SCR_003277 | SciCrunch Registry | ABRA - Assembly Based ReAligner | 2026-10-10 12:36:37 | 10 | |||||
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MetaLocGramN Resource Report Resource Website 1+ mentions |
MetaLocGramN (RRID:SCR_003154) | MetaLocGramN | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice. | subcellular localization, protein, prediction, sequence, analysis, gram-negative protein, gram-negative, gram-negative bacteria |
is listed by: OMICtools is related to: Biocatalogue - The Life Science Web Services Registry has parent organization: International Institute of Molecular and Cell Biology; Warsaw; Poland |
PMID:22705560 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01626 | SCR_003154 | SciCrunch Registry | 2026-10-10 12:36:24 | 3 | |||||||
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GeneCruiser Resource Report Resource Website 1+ mentions |
GeneCruiser (RRID:SCR_003153) | GeneCruiser | data access protocol, service resource, software resource, web service | A web service and web application for the annotation of microarray data providing integrated access to genomic information freely available from public data sources. | gene, genetic variation, probe, variation, annotation |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Broad Institute |
PMID:16030072 | Free, Freely available | OMICS_00760 | https://www.broadinstitute.org/publications/broad3691 | SCR_003153 | SciCrunch Registry | 2026-10-10 12:36:23 | 4 |
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