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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
PMut Resource Report Resource Website 50+ mentions |
PMut (RRID:SCR_010783) | PMut | software resource | A software aimed at the annotation and prediction of pathological mutations. | is listed by: OMICtools | PMID:15390262 | OMICS_00159 | SCR_010783 | 2026-02-14 02:01:49 | 80 | |||||||||
|
Integra Life Sciences Resource Report Resource Website 100+ mentions |
Integra Life Sciences (RRID:SCR_010741) | commercial organization | Commercial tissue bank for human tissues. | life science, organization, commercial, surgical instrument, neurosurgery | Commercial | grid.481865.6, nlx_97702 | https://ror.org/04t8qhn97 | SCR_010741 | Integra | 2026-02-14 02:01:48 | 384 | ||||||||
|
ALLPATHS-LG Resource Report Resource Website 100+ mentions |
ALLPATHS-LG (RRID:SCR_010742) | ALLPATHS-LG | software resource | Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. | genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:21187386 | OMICS_00007, biotools:allpaths-lg | https://bio.tools/allpaths-lg | SCR_010742 | 2026-02-14 02:02:02 | 237 | |||||||
|
Celera assembler Resource Report Resource Website 50+ mentions |
Celera assembler (RRID:SCR_010750) | Celera assembler | software resource | A de novo whole-genome shotgun (WGS) DNA sequence assembler. |
is listed by: OMICtools is related to: Canu has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00009 | SCR_010750 | 2026-02-14 02:01:49 | 56 | |||||||||
|
SOAPdenovo Resource Report Resource Website 1000+ mentions |
SOAPdenovo (RRID:SCR_010752) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, rna, dna, de novo, genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20019144 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soapdenovo, OMICS_00031, SCR_014986 | https://github.com/aquaskyline/SOAPdenovo2 https://bio.tools/soapdenovo https://sources.debian.org/src/soapdenovo/ |
SCR_010752 | SOAPdenovo2 | 2026-02-14 02:02:04 | 1299 | ||||||
|
Velvet Resource Report Resource Website 1000+ mentions |
Velvet (RRID:SCR_010755) | Velvet | sequence analysis software, data processing software, data analysis software, software application, software resource | 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 | 2026-02-14 02:02:02 | 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 | 2026-02-14 02:02:04 | 11 | |||||||
|
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 | 2026-02-14 02:01:52 | 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 | 2026-02-14 02:01:52 | 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 | 2026-02-14 02:02:07 | 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 | 2026-02-14 02:02:07 | 1 | |||||||
|
Array Studio Resource Report Resource Website 1+ mentions |
Array Studio (RRID:SCR_010970) | data processing software, analysis service resource, data analysis software, production service resource, service resource, software toolkit, software application, software 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 | 2026-02-14 02:02:08 | 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 | 2026-02-14 02:02:06 | 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 | 2026-02-14 02:02:05 | 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 | 2026-02-14 02:02:07 | 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 | 2026-02-14 02:02:09 | 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 | 2026-02-14 02:01:52 | 34 | |||||||
|
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 | 2026-02-14 02:02:05 | 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 | 2026-02-14 02:02:08 | 978 | |||||
|
LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:02:08 | 24583 |
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