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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Advanced Sequence Automated Pipeline Resource Report Resource Website 100+ mentions |
Advanced Sequence Automated Pipeline (RRID:SCR_005578) | ASAP | software resource | Software developed to provide a framework for building and executing a pipeline to preprocess next generation sequence data and variant calls. | next generation sequencing |
is listed by: OMICtools has parent organization: Vanderbilt University; Tennessee; USA |
PMID:23289815 | Free | OMICS_01033 | SCR_005578 | SciCrunch Registry | Advanced Sequence Automated Pipeline (ASAP) | 2026-10-10 12:37:22 | 324 | ||||||
|
SAMtools Text Alignment Viewer Resource Report Resource Website 1+ mentions |
SAMtools Text Alignment Viewer (RRID:SCR_005611) | SAMtools tview | software resource | Text alignment viewer software based on the GNU ncurses library that works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice. | text alignment, viewer, maq consensus, indel |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00893 | SCR_005611 | SciCrunch Registry | Text Alignment Viewer | 2026-10-10 12:37:23 | 1 | ||||||||
|
BSmooth Resource Report Resource Website 10+ mentions |
BSmooth (RRID:SCR_005693) | BSmooth | software resource | A pipeline for analyzing whole genome bisulfite sequencing (WGBS) data. | is listed by: OMICtools | OMICS_00581 | SCR_005693 | SciCrunch Registry | 2026-10-10 12:37:50 | 29 | ||||||||||
|
X-Tile Resource Report Resource Website 100+ mentions |
X-Tile (RRID:SCR_005602) | software resource | Software tool for biomarker assessment and outcome based cut point optimization. | biomarker assessment, outcome based cut point optimization |
is listed by: OMICtools has parent organization: Yale University; Connecticut; USA |
PMID:15534099 | Free, Available for download, Freely available | OMICS_00824 | http://www.tissuearray.org/rimmlab/xtile.html | SCR_005602 | SciCrunch Registry | X-tile software, X-tile | 2026-10-10 12:37:47 | 430 | ||||||
|
cancergrid-tma Resource Report Resource Website |
cancergrid-tma (RRID:SCR_005595) | cancergrid-tma | software resource | A web-based application for the management and storage of tissue microarray (TMA) images and the associated metadata. The application enables the user to navigate a grid of TMA core images within a slide, zoom and pan around an image, and enter a score constrained to a specific scoring system. The submitted scores are scored in the eXist open source database, in an XML format, which is compatible with existing TMA standards, and thus allow the data to be archived and re-used in future analysis. | tissue microarray, image |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00816 | SCR_005595 | SciCrunch Registry | Cancergrid Image Scorer | 2026-10-10 12:37:46 | 0 | ||||||||
|
Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | data or information resource, database, software resource | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | SciCrunch Registry | Sybil: Web-based software for comparative genomics | 2026-10-10 12:37:22 | 37 | ||||||
|
LookSeq Resource Report Resource Website 1+ mentions |
LookSeq (RRID:SCR_005625) | LookSeq | software resource | A web-based application for alignment visualization, browsing and analysis of genome sequence data. | alignment, visualization, browsing, analysis, genome, sequence |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00886 | SCR_005625 | SciCrunch Registry | 2026-10-10 12:37:48 | 5 | |||||||||
|
OLego Resource Report Resource Website 10+ mentions |
OLego (RRID:SCR_005811) | OLego | software resource | A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
biotools:olego, OMICS_01244 | https://bio.tools/olego | SCR_005811 | SciCrunch Registry | 2026-10-10 12:37:12 | 15 | ||||||||
|
aLFQ Resource Report Resource Website 10+ mentions |
aLFQ (RRID:SCR_005925) | software resource | An R-package for estimating absolute protein quantities from label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics data. It supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, they used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24753486 | GNU General Public License, v3 or greater | OMICS_04053 | SCR_005925 | SciCrunch Registry | aLFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data | 2026-10-10 12:37:22 | 22 | |||||||
|
PePr Resource Report Resource Website 50+ mentions |
PePr (RRID:SCR_005759) | PePr | software resource | A ChIP-Seq peak calling or differential binding analysis tool that is primarily designed for data with biological replicates. It uses a negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions. | python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24894502 | GNU General Public License, v3 | OMICS_04058, biotools:pepr | https://bio.tools/pepr | SCR_005759 | SciCrunch Registry | pepr-chip-seq, Peak Prioritization Pipeline, pepr-chip-seq: A ChIP-Seq analyzing program for biological replicates | 2026-10-10 12:37:27 | 55 | |||||
|
dna-bison Resource Report Resource Website 1+ mentions |
dna-bison (RRID:SCR_005913) | dna-bison | software resource | Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00582 | SCR_005913 | SciCrunch Registry | 2026-10-10 12:37:14 | 1 | ||||||||||
|
GraphProt Resource Report Resource Website 10+ mentions |
GraphProt (RRID:SCR_005842) | GraphProt | software resource | Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete. | sequence-binding preference, structure-binding preference, rna-binding protein, high-throughput sequencing, clip-seq, rnacompete, rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
PMID:24451197 | Free, Public | OMICS_02252, biotools:graphprot | https://bio.tools/graphprot | SCR_005842 | SciCrunch Registry | 2026-10-10 12:37:29 | 39 | ||||||
|
CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. | rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland |
PMID:21087992 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02256, biotools:clipz | https://bio.tools/clipz | SCR_005755 | SciCrunch Registry | 2026-10-10 12:37:27 | 20 | ||||||
|
JEPETTO Resource Report Resource Website 10+ mentions |
JEPETTO (RRID:SCR_005909) | JEPETTO | software resource | A Cytoscape plugin that performs integrated gene set analysis using information from interaction, pathways and processes databases. The plugin integrates information from three separate web servers specializing in enrichment analysis, pathways expansion and topological matching. It uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes. TopoGSA finds the most similar biological mechanism using the topological features of the interaction network of a user selected gene set. It is also able to suggest genes related to the query gene set using two pathway analysis servers EnrichNet and PathExpand. Both these servers are using a different topological matching algorithms that extends the query gene set with genes from the pathway databases. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results. | gene set enrichment analysis, topological analysis, interaction network, java, enrichment analysis, functional analysis, gene prioritization, integrated analysis, network analysis, interaction, pathway, process, topology, gene |
is listed by: OMICtools has parent organization: Cytoscape has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
PMID:24363376 | GNU General Public License | OMICS_02247 | SCR_005909 | SciCrunch Registry | Java Enrichment of Pathways Extended To Topology | 2026-10-10 12:37:14 | 15 | ||||||
|
PASSion Resource Report Resource Website 10+ mentions |
PASSion (RRID:SCR_005867) | PASSion | software resource | A pattern growth algorithm based pileline for splice site detection in paired-end RNA-Seq data. |
is listed by: OMICtools has parent organization: Netherlands Bioinformatics Centre |
OMICS_01246 | SCR_005867 | SciCrunch Registry | 2026-10-10 12:37:13 | 11 | ||||||||||
|
Cascade Resource Report Resource Website 50+ mentions |
Cascade (RRID:SCR_005861) | Cascade | software resource | R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, windows, gene expression, perturbation, network, diffusion, signal, temporal gene network, gene regulatory network, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Strasbourg; Strasbourg; France |
PMID:24307703 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02249, biotools:cascade | http://www-math.u-strasbg.fr/genpred/spip.php?rubrique4, https://bio.tools/cascade | SCR_005861 | SciCrunch Registry | 2026-10-10 12:37:13 | 92 | ||||||
|
IQRray Resource Report Resource Website 1+ mentions |
IQRray (RRID:SCR_006057) | IQRray | software resource | Software based on evolutionary conservation of expression profiles, implemented in R, for identification of poor quality arrays in dataset composed of arrays from many independent experiments. | r, affymetrix, microarray, quality control, evolutionary conservation, expression profile, probe |
is listed by: OMICtools has parent organization: University of Lausanne; Lausanne; Switzerland |
PMID:24451627 | Free, Public | OMICS_02244 | SCR_006057 | SciCrunch Registry | 2026-10-10 12:37:59 | 2 | |||||||
|
JATAC Resource Report Resource Website |
JATAC (RRID:SCR_003978) | JATAC | software resource | Software program for filtering duplicate 454 sequences by comparing flowgram information. | is listed by: OMICtools | PMID:23376350 | OMICS_01055 | SCR_003978 | SciCrunch Registry | 2026-10-10 12:36:43 | 0 | |||||||||
|
Antibody Resource Page Resource Report Resource Website 1+ mentions |
Antibody Resource Page (RRID:SCR_004069) | ARP | data or information resource, portal, topical portal | A complete guide to antibody research and suppliers. Serving the scientific community since 1997, the Antibody Resource Page is a guide designed by scientists for scientists to find companies that sell catalog antibodies and custom monoclonal and polyclonal antibodies. See our other pages on antibody-related databases, software, and educational websites. If you wish to suggest or update a link, please see our FAQ. | guide to antibody research and suppliers, catalog, antibodies, | is listed by: OMICtools | Free, Freely available | nif-0000-00222, OMICS_01771, SCR_011997 | SCR_004069 | SciCrunch Registry | Antibody Resource Page | 2026-10-10 12:37:02 | 4 | |||||||
|
Quantitative Enrichment of Sequence Tags Resource Report Resource Website 10+ mentions |
Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) | QuEST | software resource | A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments. | genome-wide, transcription factor binding site, chip-seq, transcription factor, binding site, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Stanford University; Stanford; California |
PMID:19160518 | OMICS_00458, biotools:quest | https://bio.tools/quest | SCR_004065 | SciCrunch Registry | Quantitative Enrichment of Sequence Tags: QuEST | 2026-10-10 12:36:57 | 49 |
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