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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Gzip Resource Report Resource Website 10+ mentions |
Gzip (RRID:SCR_009291) | Gzip | software resource | A compression utility designed to be a replacement for compress. | is listed by: OMICtools | OMICS_00961 | SCR_009291 | GNU zip | 2026-08-01 12:03:58 | 30 | |||||||||
|
SeqSaw Resource Report Resource Website |
SeqSaw (RRID:SCR_009185) | SeqSaw | software resource | A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21575597 | biotools:seqsaw, OMICS_01250 | https://bio.tools/seqsaw | SCR_009185 | SeqSaw - Short Spliced Sequence Mapping Tool | 2026-08-01 12:03:41 | 0 | ||||||
|
GAAS Resource Report Resource Website 500+ mentions |
GAAS (RRID:SCR_008967) | GAAS | software resource | An integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: Polytechnic University of Milan; Milan; Italy |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00757 | SCR_008967 | Gene Array Analyzer Software | 2026-08-01 12:04:07 | 721 | ||||||||
|
DELIMINATE Resource Report Resource Website 1+ mentions |
DELIMINATE (RRID:SCR_008956) | DELIMINATE | software resource | A practical implementation of a novel compression approach that can rapidly compress FASTA files containing genomic sequence data in a loss-less fashion. | is listed by: OMICtools | PMID:22833526 | OMICS_00953 | SCR_008956 | DELIMINATE: A fast and efficient method for loss-less compression of genomic sequences | 2026-08-01 12:03:40 | 1 | ||||||||
|
DNAzip Resource Report Resource Website 1+ mentions |
DNAzip (RRID:SCR_009032) | DNAzip | software resource | DNA sequence compression using a reference genome. |
is listed by: OMICtools has parent organization: University of California at Irvine; California; USA |
OMICS_00954 | SCR_009032 | 2026-08-01 12:03:41 | 1 | ||||||||||
|
CLIIQ Resource Report Resource Website 1+ mentions |
CLIIQ (RRID:SCR_009972) | CLIIQ | software resource | An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01272 | SCR_009972 | 2026-08-01 12:03:46 | 1 | ||||||||||
|
MSbind Resource Report Resource Website |
MSbind (RRID:SCR_009910) | MSbind | software resource | Software tool that calculates features of meta-stable RNA secondary structure target sites. |
is listed by: OMICtools has parent organization: King's College London; London; United Kingdom |
PMID:24292936 | OMICS_00390 | SCR_009910 | Msbind - Accessibility of microRNA binding sites in meta-stable RNA secondary structures in the presence of SNPs | 2026-08-01 12:04:05 | 0 | ||||||||
|
RNASEQR Resource Report Resource Website |
RNASEQR (RRID:SCR_009871) | RNASEQR | software resource | A streamlined and accurate RNA-seq sequence analysis program. | is listed by: OMICtools | OMICS_01263 | SCR_009871 | RNASEQR-a streamlined and accurate RNA-seq sequence analysis program | 2026-08-01 12:04:04 | 0 | |||||||||
|
isomiRID Resource Report Resource Website 1+ mentions |
isomiRID (RRID:SCR_009809) | isomiRID | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 4/1/14. Software providing a framework to find isomiRNAs, templated and non-templated modifications in microRNAs. |
is listed by: OMICtools has parent organization: Federal University of Rio Grande do Sul; Rio Grande do Sul; Brazil |
PMID:23946501 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00387 | SCR_009809 | 2026-08-01 12:04:11 | 5 | ||||||||
|
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 | 2026-08-01 12:04:04 | 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 | 2026-08-01 12:04:16 | 204 | ||||||
|
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 | 2026-08-01 12:04:16 | 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 | 2026-08-01 12:04:13 | 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 | 2026-08-01 12:04:17 | 1 | |||||||||
|
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 | 2026-08-01 12:04:17 | 409 | ||||||
|
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 | 2026-08-01 12:03:58 | 214 | ||||||
|
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 | 2026-08-01 12:03:55 | 1036 | |||||
|
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 | 2026-08-01 12:04:15 | 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 | 2026-08-01 12:04:16 | 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 | 2026-08-01 12:04:16 | 4 |
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