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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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nSolver Analysis Software Resource Report Resource Website 100+ mentions |
nSolver Analysis Software (RRID:SCR_003420) | nSolver Analysis Software | data processing software, software application, software resource | Data analysis software program that offers nCounter users the ability to QC, normalize, and analyze data without having to purchase additional software packages. | normalization, analysis, ncounter, os x, windows, quality control | is listed by: OMICtools | Restricted | OMICS_02309 | https://nanostring.app.box.com/v/nSolver-AdvancedAnalysis, https://nanostring.com/products/ncounter-analysis-system/ncounter-analysis-solutions/nsolver-data-analysis-support/ | SCR_003420 | 2026-09-03 04:46:18 | 405 | |||||||
|
MAGENTA Resource Report Resource Website 100+ mentions |
MAGENTA (RRID:SCR_003422) | MAGENTA | software resource | A computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes, using genome-wide genetic data as input. |
is listed by: OMICtools has parent organization: Broad Institute |
PMID:20714348 | Free, Available for download, Freely available | OMICS_00236 | SCR_003422 | Meta-Analysis Gene-set Enrichment of variaNT Associations | 2026-09-03 04:46:23 | 141 | |||||||
|
NAPPA Resource Report Resource Website 10+ mentions |
NAPPA (RRID:SCR_003419) | NAPPA | software resource | Software that enables the processing and normalization of the standard mRNA data output from the Nanostring nCounter software. | normalization, processing, nanostring, mirna, mrna, os x, windows | is listed by: OMICtools | GNU General Public License, v3 | OMICS_02310 | SCR_003419 | NAPPA: Performs the processing and normalisation of Nanostring miRNA and mRNA data | 2026-09-03 04:46:21 | 12 | |||||||
|
FadE Resource Report Resource Website 10+ mentions |
FadE (RRID:SCR_003448) | FadE | software resource | A software package designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer or nucleotide reads produced by the Illumina or 454 sequencing platforms. |
is listed by: OMICtools has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:22965123 | Free, Available for download, Freely available | OMICS_00599 | https://minituba.hegroup.org/ | SCR_003448 | fade - Estimation of position specific methylation parameters in color or nucleotide space with NR optimization | 2026-09-03 04:46:19 | 35 | ||||||
|
metagen Resource Report Resource Website 10+ mentions |
metagen (RRID:SCR_003443) | metagen | software resource | Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:17605724 | Free, Available for download, Freely available | OMICS_00238, biotools:metagen | https://www.rdocumentation.org/packages/meta/versions/4.9-6/topics/metagen | SCR_003443 | 2026-09-03 04:46:23 | 21 | ||||||
|
RevMan Resource Report Resource Website 10000+ mentions |
RevMan (RRID:SCR_003581) | RevMan | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., 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_00244 | SCR_003581 | Review Manager | 2026-09-03 04:46:25 | 12962 | ||||||||
|
PyroBayes Resource Report Resource Website 1+ mentions |
PyroBayes (RRID:SCR_003757) | PyroBayes | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A base caller for pyrosequences from the 454 Life Sciences sequencing machines. | is listed by: OMICtools | PMID:18193056 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01155 | SCR_003757 | 2026-09-03 04:46:31 | 3 | ||||||||
|
RAREMETAL Resource Report Resource Website 10+ mentions |
RAREMETAL (RRID:SCR_003573) | RAREMETAL | software resource | A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
PMID:24894501 | biotools:raremetal, OMICS_00243 | https://bio.tools/raremetal | SCR_003573 | 2026-09-03 04:46:36 | 22 | |||||||
|
Polyester Resource Report Resource Website 100+ mentions |
Polyester (RRID:SCR_003602) | data analysis software, data processing software, simulation software, software application, software resource | An R package designed to simulate RNA sequencing experiments with differential transcript expression. Given a set of annotated transcripts, it will simulate the steps of an RNA-seq experiment (fragmentation, reverse-complementing, and sequencing) and produce files containing simulated RNA-seq reads. Simulated reads can be analyzed using a choice of downstream analysis tools. Polyester has a built-in wrapper function to simulate a case/control experiment with differential transcript expression and biological replicates. Users are able to set the levels of differential expression at transcripts of their choosing. This means they know which transcripts are differentially expressed in the simulated dataset, so accuracy of statistical methods for differential expression detection can be analyzed. Polyester offers several unique features: * Built-in functionality to simulate differential expression at the transcript level * Ability to explicitly set differential expression signal strength * Simulation of small datasets, since large RNA-seq datasets can require lots of time and computing resources to analyze * Generation of raw RNA-seq reads, as opposed to alignments or transcript-level abundance estimates * Transparency/open-source code | standalone software, unix/linux, mac os x, windows, r, rna-seq | is listed by: OMICtools | OMICS_04272 | SCR_003602 | 2026-09-03 04:46:28 | 491 | ||||||||||
|
PEAR Resource Report Resource Website 500+ mentions |
PEAR (RRID:SCR_003776) | PEAR | software resource | Software for an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. | next-generation sequencing, sequence analysis |
is listed by: OMICtools has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany |
PMID:24142950 | OMICS_00674 | SCR_003776 | Pair-end read merger, PEAR: Pair-end read merger | 2026-09-03 04:46:29 | 914 | |||||||
|
SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_004013) | software resource | A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation. | c++, mrna-seq, qt |
is listed by: OMICtools has parent organization: SourceForge |
PMID:15746290 PMID:14988116 |
GNU General Public License v2 | OMICS_01289 | SCR_004013 | 2026-09-03 04:46:52 | 0 | ||||||||
|
GeneCommittee Resource Report Resource Website |
GeneCommittee (RRID:SCR_004168) | geneCommittee | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. It is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research. | dna, microarray, rna-seq, gene expression, classification, gene set, gene, gene set enrichment, functional annotation |
is listed by: OMICtools has parent organization: University of Vigo; Galicia; Spain |
PMID:24475928 | Acknowledgement requested | OMICS_02291 | https://github.com/michada/GeneCommittee | SCR_004168 | 2026-09-03 04:47:01 | 0 | ||||||
|
MSG Resource Report Resource Website 1+ mentions |
MSG (RRID:SCR_004161) | MSG | software resource | A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data. This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. | next generation sequencing, genotyping, genetic mapping, ancestry, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
PMID:21233398 | OMICS_01551 | SCR_004161 | Multiplexed shotgun genotyping, Multiplexed shotgun genotyping (MSG), MSG: Multiplexed Shotgun Genotyping | 2026-09-03 04:47:01 | 2 | |||||||
|
Babel Resource Report Resource Website 100+ mentions |
Babel (RRID:SCR_004307) | Babel | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documentedt on January 10, 2023. Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | windows, macos x |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01530 | SCR_004307 | babel: Ribosome profiling data analysis | 2026-09-03 04:47:04 | 175 | |||||||
|
PerM Resource Report Resource Website 50+ mentions |
PerM (RRID:SCR_004223) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. | Short sequencing mapping, short sequencing read, next-generation sequencing, genome, alignment, short read, abi, solid, illumina, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clippers has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:19675096 DOI:10.1093/bioinformatics/btp486 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00675, biotools:perm | https://bio.tools/perm, https://sources.debian.org/src/perm/ | SCR_004223 | PERiodic seed Mapping, Periodic seed Mapping | 2026-09-03 04:47:03 | 60 | ||||||
|
EGAPP Resource Report Resource Website 1+ mentions |
EGAPP (RRID:SCR_004189) | EGAPP | data or information resource, portal, topical portal | Initiative to develop a systematic, evidence-based process for evaluating genetic tests and other applications of genomic technology that are rapidly moving from research to use in clinical practice. A key objective of this process is to provide objective, timely, and credible information that is clearly linked to the scientific evidence on specific applications of genetic and genomic tests. The primary focus of EGAPP activities is an independent, nonfederal expert panel, the EGAPP Working Group. Other components of the EGAPP initiative include a federal interagency, the CDC staff and consultants, and an EGAPP initiative evaluation team. | genetic test, genomics, clinical, genomic technology, evaluation, public health |
is listed by: OMICtools has parent organization: Centers for Disease Control and Prevention |
OMICS_01538 | SCR_004189 | Evaluation of Genomic Applications in Practice and Prevention (EGAPP), Evaluation of Genomic Applications in Practice and Prevention | 2026-09-03 04:47:03 | 1 | ||||||||
|
HLASeq Resource Report Resource Website |
HLASeq (RRID:SCR_004185) | HLASeq | software resource | An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data. | genotyping, hla, next generation sequencing, gene, command-line, python |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01543 | SCR_004185 | 2026-09-03 04:46:59 | 0 | ||||||||
|
PASS-bis Resource Report Resource Website |
PASS-bis (RRID:SCR_004176) | PASS-bis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads. |
is listed by: OMICtools is related to: PASS |
PMID:23162053 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00587 | SCR_004176 | 2026-09-03 04:46:54 | 0 | ||||||||
|
BSRD Resource Report Resource Website 10+ mentions |
BSRD (RRID:SCR_004249) | BSRD | data or information resource, data repository, database, service resource, storage service resource | A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets. | srna target, srna, small regulatory non-coding rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23203879 | Acknowledgement requested, The community can contribute to this resource | biotools:bsrd, OMICS_01533 | https://bio.tools/bsrd | SCR_004249 | BSRD - Bacterial Small Regulatory RNA Database, Bacterial Small Regulatory RNA Database | 2026-09-03 04:47:02 | 29 | |||||
|
CDP Resource Report Resource Website 10+ mentions |
CDP (RRID:SCR_004236) | CDP | data or information resource, funding resource, portal, topical portal | National program to improve the diagnosis and assessment of cancer by moving scientific knowledge into clinical practice by coordinating and funding resources and research for the development of innovative in vitro diagnostics, novel diagnostic technologies and appropriate human specimens. The Cancer Diagnosis Program is divided into four branches: Biorepository and Biospecimen Research Branch (BBRB), Diagnostic Biomarkers and Technology Branch (DBTB), Diagnostics Evaluation Branch (DEB), and the Pathology Investigation and Resources Branch (PIRB). | cancer research, cancer funding, cancer research funding |
is listed by: OMICtools has parent organization: DCTD |
Cancer | NCI | Available to cancer researchers | OMICS_01536 | SCR_004236 | Cancer Diagnosis Program | 2026-09-03 04:47:04 | 19 |
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