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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
RASP Resource Report Resource Website 100+ mentions |
RASP (RRID:SCR_012062) | software resource | Software that uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24445369 | OMICS_03392 | SCR_012062 | SciCrunch Registry | 2026-10-24 12:46:45 | 347 | |||||||||
|
GSim Resource Report Resource Website 1+ mentions |
GSim (RRID:SCR_012061) | software resource | Free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra. | standalone software, c++ |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_03390 | SCR_012061 | SciCrunch Registry | 2026-10-24 12:46:45 | 7 | |||||||||
|
Scramble Resource Report Resource Website 10+ mentions |
Scramble (RRID:SCR_012036) | software resource | A C software implementation of SAM, BAM and CRAM file I/O. | standalone software, c, c++, fortran |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24930138 | BSD License | OMICS_04662 | SCR_012036 | SciCrunch Registry | 2026-10-24 12:46:44 | 21 | ||||||||
|
CowCoDA Resource Report Resource Website |
CowCoDA (RRID:SCR_012039) | software resource | Software that performs retention time alignment on the given set of peaks. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18715018 | OMICS_02380 | SCR_012039 | SciCrunch Registry | 2026-10-24 12:46:44 | 0 | |||||||||
|
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 | SciCrunch Registry | 2026-10-24 12:46:44 | 184 | |||||||
|
OBI-Warp Resource Report Resource Website 1+ mentions |
OBI-Warp (RRID:SCR_012041) | software resource | Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:16944896 | MIT License | OMICS_02386, biotools:obi-warp | https://bio.tools/obi-warp | SCR_012041 | SciCrunch Registry | Ordered Bijective Interpolated Warping | 2026-10-24 12:46:44 | 2 | ||||||
|
TOPP Resource Report Resource Website 10+ mentions |
TOPP (RRID:SCR_012044) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on May 23rd,2023. Software that provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17237091 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02451 | SCR_012044 | SciCrunch Registry | 2026-10-24 12:46:44 | 25 | ||||||||
|
CPFP Resource Report Resource Website 1+ mentions |
CPFP (RRID:SCR_012043) | data analysis software, data processing software, software application, software resource | Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:20189941 | OMICS_02448, biotools:cpfp | https://bio.tools/cpfp | SCR_012043 | SciCrunch Registry | Central Proteomics Facilities Pipeline | 2026-10-24 12:46:44 | 7 | |||||||
|
Antilope Resource Report Resource Website 1+ mentions |
Antilope (RRID:SCR_012046) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23rd,2023. Software that combines Lagrangian relaxation for solving an integer linear programming formulation with an adaptation of Yen''s k shortest paths algorithm. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21464512 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02481 | SCR_012046 | SciCrunch Registry | 2026-10-24 12:46:44 | 4 | ||||||||
|
swissPIT Resource Report Resource Website |
swissPIT (RRID:SCR_012045) | software resource | Software for pipelined analysis of mass spectrometry data. |
is listed by: OMICtools has parent organization: SourceForge has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:18436540 | GNU General Public License | OMICS_02452 | SCR_012045 | SciCrunch Registry | Swiss Protein Identification Toolbox | 2026-10-24 12:46:44 | 0 | ||||||||
|
ICPL ESIQuant Resource Report Resource Website |
ICPL ESIQuant (RRID:SCR_012047) | software resource | A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23454610 | biotools:icpl_esiquant, OMICS_02490 | https://bio.tools/icpl_esiquant | SCR_012047 | SciCrunch Registry | 2026-10-24 12:46:44 | 0 | ||||||||
|
Bionotate Resource Report Resource Website 1+ mentions |
Bionotate (RRID:SCR_012098) | analysis service resource, data analysis service, production service resource, service resource, software resource | An open source annotation tool for the distributed creation of a large corpus. | web app |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19232400 | GNU General Public License | OMICS_05229 | SCR_012098 | SciCrunch Registry | 2026-10-24 12:46:46 | 1 | ||||||||
|
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 | SciCrunch Registry | 2026-10-24 12:46:46 | 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 | SciCrunch Registry | Network Analysis and Inference Library | 2026-10-24 12:46:47 | 8 | ||||||
|
iMSAT Resource Report Resource Website 1+ mentions |
iMSAT (RRID:SCR_012135) | software resource | A python program that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs. | standalone software, illumina, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25281214 | OMICS_05873 | SCR_012135 | SciCrunch Registry | 2026-10-24 12:46:47 | 2 | |||||||||
|
NESmapper Resource Report Resource Website 1+ mentions |
NESmapper (RRID:SCR_012138) | software resource | A computational software tool to predict leucine-rich nuclear export signals (NESs) by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions. It is a multiplatform command-line Perl application with activity-based NES profiles. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25233087 | GNU General Public License | OMICS_05911 | SCR_012138 | SciCrunch Registry | 2026-10-24 12:46:47 | 6 | ||||||||
|
DHAC Resource Report Resource Website 1+ mentions |
DHAC (RRID:SCR_012139) | software resource | Software for clustering time-evolving networks. | standalone software, c++, matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22689777 | GNU General Public License | OMICS_05923 | SCR_012139 | SciCrunch Registry | Dynamical Hierarchical Agglomerative Clustering | 2026-10-24 12:46:47 | 2 | |||||||
|
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 | SciCrunch Registry | 2026-10-24 12:46:47 | 90 | ||||||||
|
EXCAVATOR-tool Resource Report Resource Website 1+ mentions |
EXCAVATOR-tool (RRID:SCR_012766) | EXCAVATOR-tool | software resource | A software package for the detection of copy number variants (CNVs) from whole-exome sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00332 | SCR_012766 | SciCrunch Registry | EXCAVATOR-tool: Tool for detecting CNVs from whole-exome sequencing data | 2026-10-24 12:46:53 | 7 | |||||||||
|
miRDeep* Resource Report Resource Website 10+ mentions |
miRDeep* (RRID:SCR_012960) | miRDeep* | software resource | An integrated application software tool for miRNA identification from RNA sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23221645 | GNU General Public License, v3, Acknowledgement requested | OMICS_00374 | SCR_012960 | SciCrunch Registry | 2026-10-24 12:46:57 | 23 |
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