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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CnD Resource Report Resource Website |
CnD (RRID:SCR_010818) | CnD | software resource | A program to detect copy number variants from short read sequence data. |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00338 | SCR_010818 | 2026-08-01 12:03:58 | 0 | ||||||||||
|
MAPP Resource Report Resource Website 50+ mentions |
MAPP (RRID:SCR_010775) | MAPP | software resource | Java program that predicts the impact of all possible amino acid substitutions on the function of the protein., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
NHGRI | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00132 | SCR_010775 | Multivariate Analysis of Protein Polymorphism, Multivariate Analysis of Protein Polymorphism:MAPP | 2026-08-01 12:03:57 | 58 | |||||||
|
CEQer Resource Report Resource Website 1+ mentions |
CEQer (RRID:SCR_010813) | CEQer | software resource | A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24124457 | Commercial license, Free | biotools:ceqer, OMICS_00329 | https://bio.tools/ceqer | SCR_010813 | Comparative Exome Quantification analyzer | 2026-08-01 12:04:16 | 7 | |||||
|
Oncodrive-fm Resource Report Resource Website 10+ mentions |
Oncodrive-fm (RRID:SCR_010781) | Oncodrive-fm | software resource | An approach to uncover driver genes or gene modules. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00157, biotools:oncodrivefm | https://bio.tools/oncodrivefm | SCR_010781 | 2026-08-01 12:04:16 | 14 | ||||||||
|
CRISP Resource Report Resource Website 1+ mentions |
CRISP (RRID:SCR_010759) | CRISP | software resource | A software program to detect SNPs and short indels from pooled sequencing data generated using next-generation sequencing instruments. | is listed by: OMICtools | OMICS_00057 | SCR_010759 | 2026-08-01 12:04:16 | 7 | ||||||||||
|
CloudBrush Resource Report Resource Website |
CloudBrush (RRID:SCR_010751) | CloudBrush | software resource | A De Novo Next Generation Genomic Sequence Assembler Based on String Graph and MapReduce Cloud Computing Framework. | mapreduce/hadoop | is listed by: OMICtools | PMID:23282094 | Free | OMICS_00010 | SCR_010751 | 2026-08-01 12:03:56 | 0 | |||||||
|
SSAKE Resource Report Resource Website 10+ mentions |
SSAKE (RRID:SCR_010753) | SSAKE | software resource | Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btl629 | biotools:ssake, OMICS_00033 | https://bio.tools/ssake, https://sources.debian.org/src/ssake/ | SCR_010753 | 2026-08-01 12:04:16 | 11 | |||||||
|
ComB Resource Report Resource Website 100+ mentions |
ComB (RRID:SCR_010757) | ComB | software resource | A software package designed for the downstream analysis of short read mapping data produced by the ABI SOLiD and Illumina sequencing platforms. |
is listed by: OMICtools has parent organization: Google Code |
PMID:21563978 | GNU General Public License, v2 | OMICS_00053 | SCR_010757 | 2026-08-01 12:03:56 | 103 | ||||||||
|
CopySeq Resource Report Resource Website 1+ mentions |
CopySeq (RRID:SCR_010758) | CopySeq | software resource | A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes. | java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
PMID:21085617 | biotools:copyseq, OMICS_00055 | https://bio.tools/copyseq | SCR_010758 | 2026-08-01 12:04:15 | 1 | |||||||
|
FreeBayes Resource Report Resource Website 1000+ mentions |
FreeBayes (RRID:SCR_010761) | FreeBayes | software resource | A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment. | single-nucleotide polymorphism, indel, insertion, deletion, multi-nucleotide polymorphism, complex event, composite insertion, substitution event, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:arXiv:1207.3907 | OMICS_00059, biotools:freebayes | https://bio.tools/freebayes, https://sources.debian.org/src/freebayes/ | SCR_010761 | 2026-08-01 12:04:15 | 1982 | |||||||
|
balony Resource Report Resource Website 10+ mentions |
balony (RRID:SCR_010968) | balony | software resource | Image analysis and data inspection software for agar plates generated in high-throughput yeast genetics and genomics experiments. |
is listed by: OMICtools has parent organization: Google Code |
PMID:24305553 | OMICS_00839 | SCR_010968 | balony - Software for the analysis of high-throughput solid media-based screens | 2026-08-01 12:04:18 | 11 | ||||||||
|
OligoFaktory Resource Report Resource Website 1+ mentions |
OligoFaktory (RRID:SCR_010962) | OligoFaktory | software resource | A free software for Mac OS X which designs long oligos for DNA microarrays, primers for PCR, siRNAs, and more�� | is listed by: OMICtools | Free | OMICS_00829 | SCR_010962 | 2026-08-01 12:04:18 | 1 | |||||||||
|
ProbeMaker Resource Report Resource Website 10+ mentions |
ProbeMaker (RRID:SCR_010964) | ProbeMaker | software resource | A Java software aimed at providing a framework for design and analysis of sets of oligonucleotide probes for use in multiplex assays for nucleic acid analyses and other purposes. | java |
is listed by: OMICtools has parent organization: Uppsala University; Uppsala; Sweden |
PMID:16171527 | GNU General Public License, The community can contribute to this resource, MolTools library and the AppTools library are distributed under the, GNU Lesser General Public License | OMICS_00834 | SCR_010964 | 2026-08-01 12:04:02 | 11 | |||||||
|
PROBEmer Resource Report Resource Website |
PROBEmer (RRID:SCR_010965) | PROBEmer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 1, 2014, A web-based software tool that enables selecting optimal oligos for PCR applications and multiplex detection. | is listed by: OMICtools | PMID:12824409 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00835 | SCR_010965 | 2026-08-01 12:04:18 | 0 | ||||||||
|
dPeak Resource Report Resource Website 1+ mentions |
dPeak (RRID:SCR_010855) | dPeak | software resource | A high resolution transcription factor binding site (TFBS) identification (deconvolution) algorithm. dPeak implements a probabilistic model that accurately describes ChIP-exo and ChIP-Seq data generation process for both the SET and PET assays. | chip-seq |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:24146601 | OMICS_00437 | SCR_010855 | dPeak: High Resolution TFBS Identification using ChIP-exo PET and SET ChIP-Seq Data | 2026-08-01 12:04:17 | 4 | |||||||
|
MICSA Resource Report Resource Website |
MICSA (RRID:SCR_010860) | MICSA | software resource | A software package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie (Paris). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Curie Institute; Paris; France |
biotools:micsa, OMICS_00447 | https://bio.tools/micsa | SCR_010860 | MICSA: Motif Identification for ChIP-Seq Analysis, Motif Identification for ChIP-Seq Analysis | 2026-08-01 12:03:59 | 0 | |||||||
|
CEAS Resource Report Resource Website 100+ mentions |
CEAS (RRID:SCR_010946) | CEAS | software resource | Integrates many useful tools to simplify ChIP-chip analysis for biologists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00802 | SCR_010946 | 2026-08-01 12:04:18 | 397 | |||||||||
|
EMMA2 Resource Report Resource Website 1+ mentions |
EMMA2 (RRID:SCR_010940) | EMMA2 | service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 17, 2017. A MAGE-compliant software platform for the collaborative analysis and integration of microarray data. |
is listed by: OMICtools has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:19200358 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00753 | SCR_010940 | EMMA 2 | 2026-08-01 12:04:01 | 6 | |||||||
|
XDrawChem Resource Report Resource Website |
XDrawChem (RRID:SCR_010941) | software resource | A drawing software application designed for drawing and analyzing chemical structures and reactions. | standalone software, c++, fortran |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_04961 | SCR_010941 | 2026-08-01 12:04:18 | 0 | |||||||||
|
MethLAB Resource Report Resource Website 1+ mentions |
MethLAB (RRID:SCR_010957) | MethLAB | software resource | A GUI software package for analysis of DNA methylation microarray data. |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA |
OMICS_00797 | SCR_010957 | 2026-08-01 12:04:02 | 8 |
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