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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MrBayes Resource Report Resource Website 10000+ mentions |
MrBayes (RRID:SCR_012067) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. | applet, mac os x, unix/linux, windows |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:22357727 DOI:10.1093/sysbio/sys029 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04237 | https://sources.debian.org/src/mrbayes/ | SCR_012067 | 2026-09-05 06:27:19 | 10714 | |||||||
|
OpenMS Resource Report Resource Website 100+ mentions |
OpenMS (RRID:SCR_012042) | software resource | An algorithm to align LC-MS samples and to match corresponding ion species across samples. | standalone software, mac os x, unix/linux, windows, c++, python, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:17646306 DOI:10.1186/1471-2105-9-163 |
GNU Lesser General Public License | biotools:openms | https://bio.tools/openms, https://sources.debian.org/src/openms/ | SCR_012042 | 2026-09-05 06:27:18 | 184 | |||||||
|
Pegasus-fus Resource Report Resource Website 10+ mentions |
Pegasus-fus (RRID:SCR_012118) | software resource | Software that annotates biologically functional gene fusion candidates. | standalone software, unix/linux, java, perl, python |
is used by: Cumulus is listed by: OMICtools has parent organization: SourceForge |
PMID:25183062 | OMICS_05584 | SCR_012118 | 2026-09-05 06:27:21 | 14 | |||||||||
|
NAIL Resource Report Resource Website 1+ mentions |
NAIL (RRID:SCR_012134) | software resource | A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use. | standalone software, mac os x, unix/linux, windows, matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25246431 | Apache License | OMICS_05868, biotools:nail | https://bio.tools/nail | SCR_012134 | Network Analysis and Inference Library | 2026-09-05 06:27:21 | 8 | ||||||
|
xMSanalyzer Resource Report Resource Website 50+ mentions |
xMSanalyzer (RRID:SCR_012144) | software resource | A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat. | software package, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23323971 | GNU General Public License | OMICS_06039 | SCR_012144 | 2026-09-05 06:27:21 | 90 | ||||||||
|
HeurAA Resource Report Resource Website |
HeurAA (RRID:SCR_013212) | HeurAA | software resource | Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23349847 | OMICS_00097, biotools:heuraa | https://bio.tools/heuraa | SCR_013212 | heurAA - NGS multiplexed amplicon aligner | 2026-09-05 06:27:33 | 0 | ||||||
|
FACIL Resource Report Resource Website 1+ mentions |
FACIL (RRID:SCR_004375) | FACIL | analysis service resource, data analysis service, production service resource, service resource, software resource | Genetic code prediction tool that infers the genetic code directly from any set of nucleic acid sequences and assigns a Random Forest-based reliability score to its predictions. | unix/linux | is listed by: OMICtools | PMID:21653513 | Commercial license, Free | OMICS_00299 | SCR_004375 | FACIL genetic code prediction tool, Genetic code prediction tool FACIL: Fast and Accurate genetic Code Inference and Logo | 2026-09-05 06:29:57 | 9 | ||||||
|
Phosphor Antibody Array Data Analysis Resource Report Resource Website |
Phosphor Antibody Array Data Analysis (RRID:SCR_000633) | PANDA | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies. | unix/linux, windows |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA |
PMID:18794113 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04025 | SCR_000633 | PANDA: Phosphor Antibody Array Data Analysis | 2026-09-05 06:31:11 | 0 | ||||||
|
iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-09-05 06:30:19 | 0 | ||||||
|
RUVSeq Resource Report Resource Website 100+ mentions |
RUVSeq (RRID:SCR_006263) | software resource | Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. | software package, unix/linux, mac os x, windows, r, differential expression, preprocessing, rna-seq |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25150836 | Artistic License, v2 | OMICS_05652 | SCR_006263 | RUVSeq: Remove Unwanted Variation from RNA-Seq Data | 2026-09-05 06:25:49 | 481 | |||||||
|
reseqtools Resource Report Resource Website 10+ mentions |
reseqtools (RRID:SCR_010806) | reseqtools | software resource | A Toolkit for analyzing next-generation DNA Re-Sequencing data. | java, unix/linux |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v2 | OMICS_00293 | SCR_010806 | 2026-09-05 06:26:47 | 18 | ||||||||
|
PANDAseq Resource Report Resource Website 500+ mentions |
PANDAseq (RRID:SCR_002705) | software resource, source code | Software program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. | standalone software, unix/linux, mac os x, windows, c | is listed by: OMICtools | PMID:22333067 | Free, Available for download, Freely available | OMICS_05255 | SCR_002705 | PAired-eND Assembler for DNA sequences | 2026-09-05 06:33:23 | 720 | |||||||
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, software resource, standalone software | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-09-05 06:32:20 | 0 | ||||||
|
ncdfFlow Resource Report Resource Website |
ncdfFlow (RRID:SCR_000009) | software resource | Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05617 | SCR_000009 | ncdfFlow: A package that provides ncdf based storage for flow cytometry data | 2026-09-07 08:55:13 | 0 |
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