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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Supersplat Resource Report Resource Website 1+ mentions |
Supersplat (RRID:SCR_009826) | Supersplat | software resource | An application for discovering potential splice junctions in high throughput sequencing (HTS) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01256, biotools:supersplat | https://bio.tools/supersplat | SCR_009826 | 2026-08-08 11:59:27 | 2 | ||||||||
|
SOAPsnp Resource Report Resource Website 100+ mentions |
SOAPsnp (RRID:SCR_010602) | SOAPsnp | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/gr.088013.108 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soapsnp, OMICS_00078 | https://bio.tools/soapsnp, https://sources.debian.org/src/soapsnp/ | SCR_010602 | 2026-08-08 11:59:33 | 207 | ||||||
|
TargetMiner Resource Report Resource Website 50+ mentions |
TargetMiner (RRID:SCR_010573) | TargetMiner | production service resource, software resource, data analysis service, analysis service resource, service resource | A robust tool for microRNA target prediction with systematic identification of negative examples. | is listed by: OMICtools | Free for academic use | OMICS_00419 | SCR_010573 | 2026-08-08 11:59:22 | 89 | |||||||||
|
JR-Assembler Resource Report Resource Website 1+ mentions |
JR-Assembler (RRID:SCR_010681) | JR-Assembler | software resource | An assembler for the de novo assembly of large genomes using short sequence reads via jumping extension and read remapping. | is listed by: OMICtools | PMID:23966565 | OMICS_00018 | SCR_010681 | 2026-08-08 11:59:34 | 4 | |||||||||
|
EULER-SR Resource Report Resource Website 10+ mentions |
EULER-SR (RRID:SCR_010485) | EULER-SR | software resource | Assembly package that contains a suite of software programs for correcting errors in short reads and assembling them. The assembler may take as input classical Sanger reads, 454 sequences, and Illumina reads. | fragment assembly, short read, read |
is listed by: OMICtools is listed by: Debian has parent organization: University of California at San Diego; California; USA |
PMID:18083777 DOI:10.1101/gr.7088808 |
OMICS_00015 | http://ngslib.i-med.ac.at/node/64, https://sources.debian.org/src/euler-sr/ | SCR_010485 | EULER: short reads assembler | 2026-08-08 11:59:32 | 17 | ||||||
|
MicroMUMMIE Resource Report Resource Website 1+ mentions |
MicroMUMMIE (RRID:SCR_010847) | MicroMUMMIE | software resource | Software for a specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data. |
is listed by: OMICtools has parent organization: Duke University; North Carolina; USA |
PMID:23708386 | OMICS_00401 | SCR_010847 | 2026-08-08 11:59:37 | 1 | |||||||||
|
miRDB Resource Report Resource Website 1000+ mentions |
miRDB (RRID:SCR_010848) | miRDB | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource | An online database for miRNA target prediction and functional annotations. | mirna, target, pathway, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18426918 PMID:18048393 |
OMICS_00403, biotools:miRDb | https://bio.tools/miRDB | SCR_010848 | 2026-08-08 11:59:24 | 2027 | |||||||
|
SICER Resource Report Resource Website 100+ mentions |
SICER (RRID:SCR_010843) | SICER | software resource | A clustering software package for identification of enriched domains from histone modification ChIP-Seq data. | python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: George Washington University; Washington D.C.; USA |
PMID:19505939 | biotools:sicer, OMICS_00461 | https://bio.tools/sicer | SCR_010843 | SICER: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data | 2026-08-08 11:59:37 | 420 | ||||||
|
MapSplice Resource Report Resource Website 100+ mentions |
MapSplice (RRID:SCR_010844) | MapSplice | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Kentucky; Kentucky; USA |
PMID:20802226 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mapsplice, OMICS_01243 | https://bio.tools/mapsplice | SCR_010844 | 2026-08-08 11:59:24 | 214 | ||||||
|
TargetScan Resource Report Resource Website 10000+ mentions |
TargetScan (RRID:SCR_010845) | production service resource, web service, software resource, data access protocol, data analysis service, analysis service resource, service resource | Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals. | predict, biological, target, miRNA, conserved, 8mer, 7mer, site, match seed, region, nonconserved, mismatched, pair |
is listed by: OMICtools is listed by: SoftCite has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
NIGMS GM067031; Howard Hughes Medical Institute ; NSF Graduate Research Fellowship |
PMID:26267216 | Free, Freely available | OMICS_00420 | http://www.targetscan.org/vert_71/ | SCR_010845 | TargetScanFly | 2026-08-08 11:59:38 | 11785 | |||||
|
miRNAminer Resource Report Resource Website 1+ mentions |
miRNAminer (RRID:SCR_010850) | miRNAminer | production service resource, software resource, data analysis service, analysis service resource, service resource | A web-based tool used for homologous miRNA gene search in several species. The code is available on request. |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
PMID:18215311 | Acknowledgement requested | OMICS_00409 | SCR_010850 | 2026-08-08 11:59:38 | 2 | ||||||||
|
MIRA Resource Report Resource Website 1000+ mentions |
MIRA (RRID:SCR_010731) | MIRA | software resource | Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge is required by: MITObim |
PMID:15140833 DOI:10.1101/gr.1917404 |
OMICS_00023, biotools:mira | https://bio.tools/mira | https://sources.debian.org/src/mira-assembler/ | SCR_010731 | Mimicking Intelligent Read Assembly | 2026-08-08 11:59:23 | 1047 | |||||
|
PE-Assembler Resource Report Resource Website 1+ mentions |
PE-Assembler (RRID:SCR_010732) | PE-Assembler | software resource | Software providing a method that eschews the traditional graph-based approach in favor of a simple 3'' extension approach that has potential to be massively parallelized. | is listed by: OMICtools | OMICS_00025 | SCR_010732 | 2026-08-08 11:59:34 | 3 | ||||||||||
|
QSRA Resource Report Resource Website 1+ mentions |
QSRA (RRID:SCR_010733) | QSRA | software resource | A quality-value guided de novo short read assembler. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00026, biotools:qsra | https://bio.tools/qsra | SCR_010733 | 2026-08-08 11:59:35 | 1 | ||||||||
|
rSW-seq Resource Report Resource Website 1+ mentions |
rSW-seq (RRID:SCR_010825) | rSW-seq | software resource | Designed to identify CNVs between two genomes. | is listed by: OMICtools | PMID:20718989 | OMICS_00351 | SCR_010825 | 2026-08-08 11:59:37 | 4 | |||||||||
|
SegSeq Resource Report Resource Website 10+ mentions |
SegSeq (RRID:SCR_010826) | SegSeq | software resource | An algorithm to identify chromosomal breakpoints using massively parallel next generation sequence data. |
is listed by: OMICtools has parent organization: Broad Institute |
OMICS_00352 | SCR_010826 | 2026-08-08 11:59:37 | 20 | ||||||||||
|
miRDeep Resource Report Resource Website 100+ mentions |
miRDeep (RRID:SCR_010829) | miRDeep2 | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data. | miRNA, gene, animal, clade, analysis, sequence, RNA, data | is listed by: OMICtools | Helmholtz-Alliance on Systems Biology ; Helmholtz Association ; German Ministry of Education and Research ; Senate of Berlin ; China Scholarship Council ; Max Delbrück Centrum Systems Biology Network |
PMID:18392026 PMID:21911355 |
Free, Available for download, Freely available | OMICS_00373 | https://github.com/rajewsky-lab/mirdeep2 | SCR_010829 | 2026-08-08 11:59:37 | 182 | |||||
|
SAPRED Resource Report Resource Website 1+ mentions |
SAPRED (RRID:SCR_010785) | SAPRED | software resource | Offers the researchers an automatic pipeline to predict the disease-association of SAPs. |
is listed by: OMICtools has parent organization: Peking University; Beijing; China |
PMID:17384424 | OMICS_00161 | SCR_010785 | SAP Disease-Association Predictor | 2026-08-08 11:59:36 | 4 | ||||||||
|
SNAP - Effects of Single Amino Acid Substitutions on Protein Function Resource Report Resource Website 10+ mentions |
SNAP - Effects of Single Amino Acid Substitutions on Protein Function (RRID:SCR_010786) | SNAP | production service resource, software resource, data analysis service, analysis service resource, service resource | A method for evaluating effects of single amino acid substitutions on protein function. |
is listed by: OMICtools has parent organization: Columbia University; New York; USA |
PMID:17526529 | Acknowledgement requested | OMICS_00162 | SCR_010786 | 2026-08-08 11:59:24 | 38 | ||||||||
|
TransFIC Resource Report Resource Website 10+ mentions |
TransFIC (RRID:SCR_010788) | TransFIC | production service resource, software resource, data analysis service, software application, analysis service resource, data analysis software, service resource, data processing software | A method to transform Functional Impact scores taking into account the differences in basal tolerance to germline SNVs of genes that belong to different functional classes. |
is listed by: OMICtools has parent organization: Pompeu Fabra University; Barcelona; Spain |
Cancer | OMICS_00164 | SCR_010788 | TRANSformed Functional Impact for Cancer | 2026-08-08 11:59:36 | 14 |
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