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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | SciCrunch Registry | 2026-10-31 12:15:05 | 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 | SciCrunch Registry | Msbind - Accessibility of microRNA binding sites in meta-stable RNA secondary structures in the presence of SNPs | 2026-10-31 12:15:01 | 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 | SciCrunch Registry | RNASEQR-a streamlined and accurate RNA-seq sequence analysis program | 2026-10-31 12:15:00 | 0 | |||||||||
|
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 | SciCrunch Registry | 2026-10-31 12:15:07 | 207 | ||||||
|
TargetMiner Resource Report Resource Website 50+ mentions |
TargetMiner (RRID:SCR_010573) | TargetMiner | analysis service resource, data analysis service, production service resource, service resource, software 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 | SciCrunch Registry | 2026-10-31 12:15:09 | 89 | |||||||||
|
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 | SciCrunch Registry | Mimicking Intelligent Read Assembly | 2026-10-31 12:15:08 | 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 | SciCrunch Registry | 2026-10-31 12:15:10 | 3 | ||||||||||
|
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 | SciCrunch Registry | 2026-10-31 12:15:07 | 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 | SciCrunch Registry | EULER: short reads assembler | 2026-10-31 12:15:05 | 17 | ||||||
|
openADAM Resource Report Resource Website |
openADAM (RRID:SCR_002018) | openADAM | data management software, software application, software resource | A web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Genome-Wide Human SNP Array platforms. | php, perl, front end, affymetrix genechip mapping array, affymetrix genome-wide human snp array, data management, affymetrix, snp, genome-wide association |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19117518 | Free, Available for download, Freely available | OMICS_01921 | SCR_002018 | SciCrunch Registry | 2026-10-31 12:13:00 | 0 | |||||||
|
flowTrans Resource Report Resource Website 1+ mentions |
flowTrans (RRID:SCR_002093) | software resource | Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21050468 | Free, Available for download, Freely available | OMICS_05612 | SCR_002093 | SciCrunch Registry | flowTrans - Parameter Optimization for Flow Cytometry Data Transformation | 2026-10-31 12:13:01 | 5 | |||||||
|
SNAP - SNP Annotation and Proxy Search Resource Report Resource Website 100+ mentions |
SNAP - SNP Annotation and Proxy Search (RRID:SCR_002127) | SNAP | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots | gene, genetic, genomic, r, oracle, single nucleotide polymorphism, linkage disequilibrium, genotypeing array, physical distance, membership, proxy, plot |
is listed by: OMICtools is listed by: Genetic Analysis Software is related to: International HapMap Project is related to: 1000 Genomes: A Deep Catalog of Human Genetic Variation has parent organization: Broad Institute |
NHLBI N01-HC-65226 | PMID:18974171 | Free, Freely Available | OMICS_01927, nlx_154638 | http://www.broad.mit.edu/mpg/snap/ | SCR_002127 | SciCrunch Registry | SNAP (SNP Annotation and Proxy Search), SNAP 2, SNP Annotation and Proxy Search | 2026-10-31 12:13:01 | 146 | ||||
|
AffyPipe Resource Report Resource Website 1+ mentions |
AffyPipe (RRID:SCR_002032) | software resource | An open-source software pipeline for Affymetrix Axiom genotyping workflow. | affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Italian Ministry of Education University and Research 505/Ric; project GenHome ; European Union FP7 project Gene2Farm 289592 |
PMID:25028724 | Free, Available for download, Freely available | biotools:affypipe, OMICS_05203 | https://bio.tools/affypipe | SCR_002032 | SciCrunch Registry | AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow | 2026-10-31 12:13:00 | 5 | |||||
|
CanSNPer Resource Report Resource Website 10+ mentions |
CanSNPer (RRID:SCR_001980) | software resource | Software that is a hierarchical genotype classifier of clonal pathogens. | python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24574113 | Free, Available for download, Freely available | biotools:cansnper, OMICS_03706 | https://bio.tools/cansnper | SCR_001980 | SciCrunch Registry | 2026-10-31 12:12:59 | 18 | |||||||
|
DMET-Analyzer Resource Report Resource Website 1+ mentions |
DMET-Analyzer (RRID:SCR_002030) | DMET-Analyzer | software resource | Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way. | drug, metabolism, enzyme, transporter, affymetrix, variation, genome, clinical, affymetrix dmet, single nucleotide polymorphism, annotation, analysis, pharmacogenomic, pathway |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23035929 | Free, Available for download, Freely available | OMICS_01920 | SCR_002030 | SciCrunch Registry | DMETANALYZER, DMETANALYZER - A tool for supporting pharmacogenomics data analysis | 2026-10-31 12:13:00 | 1 | ||||||
|
SNVer Resource Report Resource Website 50+ mentions |
SNVer (RRID:SCR_002061) | data analysis software, data processing software, software application, software resource | Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data. | statistical analysis software, sequencing, dna, whole-exome, whole-genome, variant, bio.tools |
lists: SAMTOOLS is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:21813454 | Free, Available for download, Freely available | OMICS_00076, biotools:snver | https://sourceforge.net/projects/snver/, https://bio.tools/snver | SCR_002061 | SciCrunch Registry | 2026-10-31 12:13:01 | 52 | |||||||
|
ChIPSeq Peak Finder Resource Report Resource Website 1+ mentions |
ChIPSeq Peak Finder (RRID:SCR_002081) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | chipseq, sequencing, dna, analysis, solexa, illumina |
is listed by: OMICtools is listed by: Debian has parent organization: Genome Institute of Singapore; Singapore; Singapore |
PMID:27863463 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00434 | https://sources.debian.org/src/chip-seq/ | SCR_002081 | SciCrunch Registry | ChIPSeq Toolbox | 2026-10-31 12:13:01 | 1 | ||||||
|
PyroHMMvar Resource Report Resource Website 1+ mentions |
PyroHMMvar (RRID:SCR_002073) | PyroHMMvar | software resource | A software program to call short indels and SNPs for Ion Torrent and 454 data. |
is listed by: OMICtools has parent organization: Google Code |
PMID:23995392 | Free, Available for download, Freely available | OMICS_00069 | https://code.google.com/p/pyrohmmvar/ | SCR_002073 | SciCrunch Registry | 2026-10-31 12:13:01 | 1 | |||||||
|
flowMap Resource Report Resource Website 1+ mentions |
flowMap (RRID:SCR_002269) | software resource | Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process. | software package, mac os x, unix/linux, windows, r, flow cytometry, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_05600 | SCR_002269 | SciCrunch Registry | flowMap - A probabilistic algorithm for matching and comparing multiple flow cytometry samples | 2026-10-31 12:13:03 | 5 | ||||||||
|
Cake Resource Report Resource Website 10+ mentions |
Cake (RRID:SCR_002133) | software resource | A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. | standalone software, unix/linux, mac os x, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23803469 | Free, Available for download, Freely available | OMICS_03613, biotools:cake | https://bio.tools/cake | SCR_002133 | SciCrunch Registry | 2026-10-31 12:13:01 | 11 |
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