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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
OmicCircos Resource Report Resource Website 50+ mentions |
OmicCircos (RRID:SCR_003292) | software resource | An R software application and package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. | standalone software, unix/linux, mac os x, windows, r, annotation, statistical method, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24526832 | Free, Available for download, Freely available | OMICS_04659 | http://www.bioconductor.org/packages/release/bioc/html/OmicCircos.html | SCR_003292 | OmicCircos: High-quality circular visualization of omic data | 2026-08-01 12:02:07 | 79 | ||||||
|
MIPgen Resource Report Resource Website 10+ mentions |
MIPgen (RRID:SCR_003325) | software resource | Software for a fast, simple way to generate designs for MIP assays targeting hundreds or thousands of genomic loci in parallel. Packaged with MIPgen are scripts that aid in visualization of MIP designs and processing of MIP sequence reads to SAM files that can then be passed through any standard variant calling pipeline. | standalone software, c++, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:24867941 | Free, Available for download, Freely available | OMICS_04657, biotools:mipgen | https://github.com/shendurelab/MIPGEN, https://bio.tools/mipgen | SCR_003325 | MIPgen - One stop MIP design and analysis | 2026-08-01 12:02:08 | 48 | ||||||
|
PoPoolation2 Resource Report Resource Website 100+ mentions |
PoPoolation2 (RRID:SCR_003284) | software resource | Software to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, next generation sequencing, population genetics, population genomics, statistics, toolkit, population |
is listed by: OMICtools has parent organization: Google Code |
PMID:22025480 | Free, Available for download, Freely available | OMICS_05824 | SCR_003284 | 2026-08-01 12:02:29 | 242 | ||||||||
|
DAFGA Resource Report Resource Website 1+ mentions |
DAFGA (RRID:SCR_003319) | software resource | A python script package which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. It provides gene-specific parameter sets for OTU clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME or Mothur. | standalone software, python | is listed by: OMICtools | PMID:24939150 | Free, Available for download, Freely available | OMICS_04654 | SCR_003319 | DAFGA: Diversity Analysis of Functional Gene Amplicons, Diversity analysis of Functional Gene Amplicons | 2026-08-01 12:02:29 | 1 | |||||||
|
Snakemake Resource Report Resource Website 100+ mentions |
Snakemake (RRID:SCR_003475) | Snakemake | software resource | A Python based language and execution environment for make-like workflows. The system supports the use of automatically inferred multiple named wildcards (or variables) in input and output filenames. | python, workflow, bio.tools |
is used by: RiboSnake is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22908215 DOI:10.1093/bioinformatics/bts480 |
Free, Available for download, Freely available | OMICS_02299, biotools:snakemake | https://snakemake.github.io/ | SCR_003475 | snakemake - A Python based language and execution environment for make-like workflows | 2026-08-01 12:02:31 | 393 | |||||
|
PheWAS R Package Resource Report Resource Website 1+ mentions |
PheWAS R Package (RRID:SCR_003512) | software resource | Software package contains methods for performing Phenome-Wide Association Study. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Vanderbilt University; Tennessee; USA |
PMID:20335276 | Free | OMICS_00242, biotools:phewas | https://bio.tools/phewas | SCR_003512 | Phenome-Wide Association Study | 2026-08-01 12:02:31 | 6 | ||||||
|
NGSANE Resource Report Resource Website 10+ mentions |
NGSANE (RRID:SCR_003478) | NGSANE | software resource | Software providing a Linux-based High Performance Computing (HPC) enabled framework for high-throughput data analysis that minimizes overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing raw sequence data. | next generation sequencing | is listed by: OMICtools | PMID:24470576 | BSD License, v3 | OMICS_02298 | SCR_003478 | Next Generation Sequencing ANalysis for Enterprises | 2026-08-01 12:02:31 | 10 | ||||||
|
SNAPE-pooled Resource Report Resource Website 1+ mentions |
SNAPE-pooled (RRID:SCR_003476) | software resource | Software that computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome. | standalone software |
is listed by: OMICtools has parent organization: Google Code |
PMID:22992255 | GNU General Public License, v3 | OMICS_05820 | SCR_003476 | snape-pooled: Computes the minor allele frequency spectrum in pooled DNA (sequenced) samples | 2026-08-01 12:02:13 | 8 | |||||||
|
Bpipe Resource Report Resource Website 10+ mentions |
Bpipe (RRID:SCR_003471) | Bpipe | software resource | Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments. | genetics, dna, analysis, cluster, workflow, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22500002 | Free, Available for download, Freely available | biotools:bpipe, OMICS_02301 | https://github.com/ssadedin/bpipe | SCR_003471 | bpipe - A tool for running and managing bioinformatics pipelines | 2026-08-01 12:02:21 | 13 | |||||
|
Parseq Resource Report Resource Website 1+ mentions |
Parseq (RRID:SCR_003464) | Parseq | software resource | Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders. | rna-seq, genome, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Sorbonne University; Paris; France |
PMID:24470570 | Free, Available for download, Freely available | biotools:parseq, OMICS_02302 | https://bio.tools/parseq | SCR_003464 | 2026-08-01 12:02:12 | 2 | ||||||
|
GBSA Resource Report Resource Website 1+ mentions |
GBSA (RRID:SCR_003413) | GBSA | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Software for analyzing whole-genome bisulfite sequencing data. |
is listed by: OMICtools has parent organization: National University of Singapore; Singapore; Singapore |
PMID:23268441 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00600 | SCR_003413 | Genome-Wide Bisulfite Sequencing Analyser Software, GBSA - Genome-Wide Bisulfite Sequencing Analyser Software | 2026-08-01 12:02:21 | 2 | |||||||
|
MultiPhen Resource Report Resource Website 10+ mentions |
MultiPhen (RRID:SCR_003498) | software resource | Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model). | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:22567092 | GNU General Public License, v2 | biotools:multiphen, OMICS_04397 | https://bio.tools/multiphen | SCR_003498 | MultiPhen: a package for the genetic association testing of multiple phenotypes | 2026-08-01 12:02:31 | 29 | ||||||
|
EBSeq Resource Report Resource Website 500+ mentions |
EBSeq (RRID:SCR_003526) | EBSeq | software resource | Software R package for RNA-Seq Differential Expression Analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:23428641 DOI:10.1093/bioinformatics/btt087 |
biotools:ebseq, OMICS_01307 | https://bio.tools/ebseq, https://sources.debian.org/src/r-bioc-ebseq/ | SCR_003526 | 2026-08-01 12:02:14 | 577 | |||||||
|
MetaSKAT Resource Report Resource Website 10+ mentions |
MetaSKAT (RRID:SCR_003489) | MetaSKAT | software resource | A R package for multiple marker meta-analysis. |
is listed by: OMICtools has parent organization: Harvard T.H. Chan School of Public Health |
PMID:23768515 | Free | OMICS_00241 | SCR_003489 | 2026-08-01 12:02:22 | 31 | ||||||||
|
Savant Resource Report Resource Website 50+ mentions |
Savant (RRID:SCR_003488) | Savant | software resource | Next-generation genome browser software designed for the latest generation of genome data. |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
Free, Available for download, Freely available | OMICS_00923 | https://github.com/compbio-UofT/savant | SCR_003488 | 2026-08-01 12:02:13 | 64 | ||||||||
|
jmzTab Resource Report Resource Website 1+ mentions |
jmzTab (RRID:SCR_003481) | software resource | A Java interface to the mzTab data exchange format for reporting a summary of proteomics results. | standalone software, mac os x, unix/linux, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24659499 | Apache License, v2 | OMICS_04542, biotools:jmztab | https://bio.tools/jmztab | SCR_003481 | 2026-08-01 12:02:31 | 1 | |||||||
|
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 | 2026-08-01 12:02:21 | 140 | |||||||
|
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 | 2026-08-01 12:02:21 | 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 | 2026-08-01 12:02:30 | 34 | ||||||
|
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 | 2026-08-01 12:02:21 | 18 |
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