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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MIREAP Resource Report Resource Website 100+ mentions |
MIREAP (RRID:SCR_013025) | MIREAP | software resource | A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00376 | SCR_013025 | 2026-08-01 12:04:43 | 371 | |||||||||
|
MIReNA Resource Report Resource Website 1+ mentions |
MIReNA (RRID:SCR_013024) | MIReNA | software resource | A software tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. | is listed by: OMICtools | PMID:20591903 | Acknowledgement requested, CeCILL license | OMICS_00377 | SCR_013024 | 2026-08-01 12:04:54 | 8 | ||||||||
|
MIG Resource Report Resource Website 1+ mentions |
MIG (RRID:SCR_012972) | MIG | software resource | Allows the user to conveniently compare data from many loci., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00942 | SCR_012972 | Multi-Image Genome | 2026-08-01 12:04:42 | 1 | ||||||||
|
EDNA Resource Report Resource Website 10+ mentions |
EDNA (RRID:SCR_012981) | EDNA | software resource | Software for Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23990411 | Creative Commons Attribution NonCommercial License, v2 | OMICS_00974 | SCR_012981 | EDNA - Energy Based Multiple Sequence Alignment (MSA) for Binding Sites | 2026-08-01 12:04:54 | 34 | ||||||
|
cn.mops Resource Report Resource Website 10+ mentions |
cn.mops (RRID:SCR_013036) | cn.mops | software resource | A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
biotools:cn.mops, OMICS_00335 | https://bio.tools/cn.mops | SCR_013036 | Copy Number estimation by a Mixture Of PoissonS | 2026-08-01 12:04:44 | 10 | |||||||
|
SAMZIP Resource Report Resource Website |
SAMZIP (RRID:SCR_012980) | SAMZIP | software resource | An encoding and decoding tool for Sequence Alignment/Map (SAM) files. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22164252 | OMICS_00967 | SCR_012980 | 2026-08-01 12:04:43 | 0 | |||||||||
|
SAMMate Resource Report Resource Website 10+ mentions |
SAMMate (RRID:SCR_013037) | SAMMate | software resource | An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
biotools:sammate, OMICS_01264 | https://bio.tools/sammate | SCR_013037 | 2026-08-01 12:04:54 | 11 | ||||||||
|
SHREC Resource Report Resource Website 10+ mentions |
SHREC (RRID:SCR_013009) | SHREC | software resource | A bioinformatics tool for error correction of HTS read data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01110 | SCR_013009 | 2026-08-01 12:04:43 | 13 | ||||||||||
|
hiCtools Resource Report Resource Website |
hiCtools (RRID:SCR_013010) | hiCtools | software resource | This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_00522 | SCR_013010 | 2026-08-01 12:04:54 | 0 | |||||||||
|
LOCAS Resource Report Resource Website 1+ mentions |
LOCAS (RRID:SCR_013064) | LOCAS | software resource | A software to assemble short reads of next generation sequencing technologies at low coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21858125 | OMICS_00019, biotools:locas | https://bio.tools/locas | SCR_013064 | 2026-08-01 12:04:55 | 2 | |||||||
|
VDJFasta Resource Report Resource Website 1+ mentions |
VDJFasta (RRID:SCR_013069) | VDJFasta | software resource | Bioinformatics Perl extension for the analysis of antibody variable domain repertoires. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19875695 | OMICS_00004 | SCR_013069 | 2026-08-01 12:04:44 | 8 | |||||||||
|
VCAKE Resource Report Resource Website 1+ mentions |
VCAKE (RRID:SCR_013060) | VCAKE | software resource | A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00037 | SCR_013060 | 2026-08-01 12:04:55 | 4 | ||||||||||
|
PRICE Resource Report Resource Website 100+ mentions |
PRICE (RRID:SCR_013063) | PRICE | software resource | Software for a de novo genome assembler implemented in C++. | c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Francisco; California; USA |
OMICS_01430, biotools:price | https://bio.tools/price | SCR_013063 | Paired-Read Iterative Contig Extension | 2026-08-01 12:04:44 | 162 | |||||||
|
HiTC Resource Report Resource Website 50+ mentions |
HiTC (RRID:SCR_013175) | HiTC | software resource | Software package to explore high-throughput ''C'' data such as 5C or Hi-C. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00524 | SCR_013175 | 2026-08-01 12:04:56 | 83 | ||||||||||
|
CoNIFER Resource Report Resource Website 100+ mentions |
CoNIFER (RRID:SCR_013213) | CoNIFER | software resource | Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. |
is listed by: OMICtools has parent organization: SourceForge |
Commercial license | OMICS_00330 | SCR_013213 | Copy Number Inference From Exome Reads | 2026-08-01 12:04:46 | 195 | ||||||||
|
RDXplorer Resource Report Resource Website 1+ mentions |
RDXplorer (RRID:SCR_013290) | RDXplorer | software resource | A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
biotools:RDXplorer, OMICS_00349 | https://bio.tools/RDXplorer | SCR_013290 | 2026-08-01 12:04:47 | 7 | ||||||||
|
PIA Resource Report Resource Website |
PIA (RRID:SCR_013267) | PIA | software resource | A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00676 | SCR_013267 | 2026-08-01 12:04:46 | 0 | |||||||||
|
Wgsim Resource Report Resource Website 100+ mentions |
Wgsim (RRID:SCR_013269) | Wgsim | software resource | A small tool for simulating sequence reads from a reference genome. | is listed by: OMICtools | OMICS_00260 | SCR_013269 | 2026-08-01 12:04:57 | 161 | ||||||||||
|
SOAPdenovo-Trans Resource Report Resource Website 100+ mentions |
SOAPdenovo-Trans (RRID:SCR_013268) | SOAPdenovo-Trans | software resource | A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01324 | SCR_013268 | 2026-08-01 12:04:47 | 170 | |||||||||
|
BRAT Resource Report Resource Website 50+ mentions |
BRAT (RRID:SCR_013159) | BRAT | software resource | BRAT is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer. | is listed by: OMICtools | OMICS_00577 | SCR_013159 | Bisulfite-treated Reads Analysis Tool | 2026-08-01 12:04:45 | 53 |
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