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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Velvet Resource Report Resource Website 1000+ mentions |
Velvet (RRID:SCR_010755) | Velvet | data analysis software, software application, software resource, sequence analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | de novo, genomic, assembly, short, read, sequencing, de Bruijn, graph, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Velvet-SC is related to: shovill has parent organization: European Bioinformatics Institute |
EMBL | PMID:18349386 DOI:10.1101/gr.074492.107 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00038, biotools:velvet | https://www.ebi.ac.uk/~zerbino/velvet/, https://bio.tools/velvet, https://sources.debian.org/src/velvet/ | SCR_010755 | 2026-08-01 12:04:15 | 1036 | |||||
|
Atlas2 Resource Report Resource Website 10+ mentions |
Atlas2 (RRID:SCR_010756) | software resource | A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in WECS data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Baylor University; Texas; USA |
PMID:22239737 | biotools:atlas_suite, OMICS_00051 | https://bio.tools/atlas_suite | SCR_010756 | Atlas Suite | 2026-08-01 12:04:16 | 11 | |||||||
|
FamSeq Resource Report Resource Website |
FamSeq (RRID:SCR_010760) | FamSeq | software resource | A computational tool for calculating probability of variants in family-based sequencing data. | c++ |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center |
PMID:23426633 | OMICS_00058 | SCR_010760 | Family-Based Sequencing Program | 2026-08-01 12:03:56 | 0 | |||||||
|
GenePix Pro Resource Report Resource Website 500+ mentions |
GenePix Pro (RRID:SCR_010969) | GenePix Pro | software resource | Industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and intuitive workflows. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00840 | SCR_010969 | 2026-08-01 12:04:19 | 627 | ||||||||||
|
OligoArray Resource Report Resource Website 10+ mentions |
OligoArray (RRID:SCR_010961) | OligoArray | software resource | A free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:12799432 | OMICS_00828, biotools:oligoarray | https://bio.tools/oligoarray | SCR_010961 | OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach, OligoArray 2.1: Genome-scale oligonucleotide design for microarrays | 2026-08-01 12:04:02 | 38 | ||||||
|
Picky Resource Report Resource Website 10+ mentions |
Picky (RRID:SCR_010963) | Picky | software resource | A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. |
is listed by: OMICtools has parent organization: Iowa State University; Iowa; USA |
NSF DBI0850195 | PMID:15180932 PMID:19849862 PMID:20406469 |
Free, Public, Acknowledgement requested | OMICS_00833 | SCR_010963 | Picky: Optimal Oligonucleotide Design and Analysis | 2026-08-01 12:04:19 | 37 | ||||||
|
ROSO Resource Report Resource Website 1+ mentions |
ROSO (RRID:SCR_010967) | ROSO | software resource | A software to design optimized oligonucleotide probes (size over 25 nucleotides) for microarrays. |
is listed by: OMICtools has parent organization: PRABI |
PMID:14734320 | Free to non-profit users, On request | OMICS_00838 | SCR_010967 | ROSO - A friend for your design, Recherche et Optimisation de Sondes Oligonucl��otidiques, Recherche et Optimisation de Sondes Oligonucleotidiques | 2026-08-01 12:04:02 | 1 | |||||||
|
Array Studio Resource Report Resource Website 1+ mentions |
Array Studio (RRID:SCR_010970) | software toolkit, data analysis software, service resource, software application, production service resource, software resource, data processing software, analysis service resource | Software package which provides statistics and visualization for analysis of high dimensional quantification data including microarray or RTPCR data or Taqman data, genotype data including SNP or Copy Number data and Next Generation Sequencing data. Provides integrated environment for analyzing and visualizing high dimensional data. | Statistic, visualization, data, analysis, quantification, integrated environment, microarray data, RTPCR data, Taqman data, genotype data, copy number data, next generation sequencing data | Free, Available for download, Freely available | OMICS_00850 | https://omicsoftdocs.github.io/ArraySuiteDoc/tutorials/ArrayStudio/ArrayStudio/ | http://www.omicsoft.com/array-studio.php | SCR_010970 | 2026-08-01 12:04:02 | 5 | ||||||||
|
HMCan Resource Report Resource Website 10+ mentions |
HMCan (RRID:SCR_010858) | HMCan | software resource | A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:24021381 | biotools:hmcan, OMICS_00443 | https://bio.tools/hmcan | SCR_010858 | Histone Modification in Cancer | 2026-08-01 12:04:18 | 13 | ||||||
|
COPS Resource Report Resource Website 100+ mentions |
COPS (RRID:SCR_010852) | COPS | software resource | Software for detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets. |
is listed by: OMICtools has parent organization: Heidelberg University; Baden-Wurttemberg; Germany |
PMID:23272209 | OMICS_00479 | SCR_010852 | COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets | 2026-08-01 12:03:59 | 267 | ||||||||
|
GenomeStudio Resource Report Resource Website 1000+ mentions |
GenomeStudio (RRID:SCR_010973) | GenomeStudio | software resource | Visualize and analyze data generated by all of Illumina''s platforms. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00854 | SCR_010973 | 2026-08-01 12:04:18 | 2954 | ||||||||||
|
ComBat Resource Report Resource Website 1000+ mentions |
ComBat (RRID:SCR_010974) | ComBat | software resource | Adjusting batch effects in microarray expression data using Empirical Bayes methods. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00857 | SCR_010974 | 2026-08-01 12:04:19 | 3492 | ||||||||||
|
MicroGen Resource Report Resource Website 10+ mentions |
MicroGen (RRID:SCR_010976) | MicroGen | software resource | Software application package for a Minimum Information About Microarray Experiments (MIAME) compliant web-based information system for managing all the information completely characterizing spotted microarray experiments and the produced data. | microarray |
is listed by: OMICtools has parent organization: Polytechnic University of Milan; Milan; Italy |
PMID:16351755 | OMICS_00867 | SCR_010976 | MicroGen - a Web Server for Microarray Experiments | 2026-08-01 12:04:02 | 34 | |||||||
|
E-RANGE Resource Report Resource Website |
E-RANGE (RRID:SCR_010856) | E-RANGE | software resource | A Python package for doing RNA-seq and ChIP-seq (hence the dual-use). | is listed by: OMICtools | OMICS_00439 | SCR_010856 | 2026-08-01 12:03:59 | 0 | ||||||||||
|
FindPeaks Resource Report Resource Website 100+ mentions |
FindPeaks (RRID:SCR_010857) | FindPeaks | software resource | Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis). | chip-seq |
is listed by: OMICtools has parent organization: SourceForge |
BC Cancer Agency ; Michael Smith Foundation for Health Research |
OMICS_00440 | SCR_010857 | 2026-08-01 12:04:17 | 328 | ||||||||
|
CoCo Resource Report Resource Website 500+ mentions |
CoCo (RRID:SCR_010947) | CoCo | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2021.A computational tool that allows the user to search, visualise and store different data associated with gene expression. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:17234641 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00805, biotools:CoCo | https://bio.tools/CoCo | SCR_010947 | ChIP-on-chip online | 2026-08-01 12:04:02 | 978 | |||||
|
LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data processing software, data analysis software, software application, software resource | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-08-01 12:04:18 | 24583 | ||||||
|
Mayday Resource Report Resource Website 10+ mentions |
Mayday (RRID:SCR_010945) | Mayday | software resource | Software providing a workbench for visualization, analysis and storage of microarray data. It features a graphical user interface and supports the development and integration of existing and new analysis methods. Besides the infrastructural core functionality, Mayday offers a variety of plug-ins, such as various interactive viewers, a connection to the R statistical environment, a connection to SQL-based databases, and different clustering methods, including phylogenetic methods. In addition, so-called meta information objects are provided for annotation of the microarray data allowing integration of data from different sources. This meta information can be used to enhance visualizations, such as in the enhanced heatmap visualization. Written in the Java programming language, Mayday is extremely portable and runs on all platforms supporting the Java runtime environment 1.6. | java |
is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
GNU General Public License, Plug-ins:, GNU Lesser General Public License | OMICS_00773 | SCR_010945 | Mayday - Microarray Data Analysis | 2026-08-01 12:04:18 | 14 | |||||||
|
RPPanalyzer Resource Report Resource Website 1+ mentions |
RPPanalyzer (RRID:SCR_010959) | RPPanalyzer | software resource | A statistical tool developed to read reverse-phase protein array data, to perform the basic data analysis and to visualize the resulting biological information. | is listed by: OMICtools | GNU Lesser General Public License, v2, 2.1, 3 | OMICS_00815 | SCR_010959 | RPPanalyzer: Reads annotates and normalizes reverse phase protein array data | 2026-08-01 12:04:19 | 8 | ||||||||
|
BioTile Resource Report Resource Website |
BioTile (RRID:SCR_010953) | BioTile | software resource | A Perl based tool for the identification of differentially enriched regions in tiling microarray data. | is listed by: OMICtools | OMICS_00791 | SCR_010953 | 2026-08-01 12:04:18 | 0 |
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