Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
iPapers Resource Report Resource Website |
iPapers (RRID:SCR_012103) | software resource | Software application that manages many PDF files of articles, whose information can be obtained by PubMed. | standalone software, mac os x |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05280 | SCR_012103 | 2026-07-25 12:07:31 | 0 | ||||||||||
|
PhyloTreePruner Resource Report Resource Website 10+ mentions |
PhyloTreePruner (RRID:SCR_012069) | software resource | A utility that uses a phylogenetic approach to refine orthology inferences made by graph-based (or other) methods. | applet |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24250218 | OMICS_04250 | SCR_012069 | 2026-07-25 12:07:26 | 32 | |||||||||
|
Connecting Overlapped Pair-End reads Resource Report Resource Website 1+ mentions |
Connecting Overlapped Pair-End reads (RRID:SCR_012102) | COPE | software resource | An efficient software tool to connect overlapping pair-end reads using k-mer frequencies. | standalone software, c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23044551 | GNU General Public License, v3 | OMICS_05256 | ftp://ftp.genomics.org.cn/pub/cope | SCR_012102 | Connecting Overlapped Pair-End | 2026-07-25 12:07:28 | 3 | |||||
|
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 | 2026-07-25 12:07:30 | 323 | |||||||||
|
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 | 2026-07-25 12:07:27 | 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 | 2026-07-25 12:07:29 | 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 | 2026-07-25 12:07:25 | 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 | 2026-07-25 12:07:25 | 174 | |||||||
|
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 | Ordered Bijective Interpolated Warping | 2026-07-25 12:07:29 | 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 | 2026-07-25 12:07:29 | 25 | ||||||||
|
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 | 2026-07-25 12:07:27 | 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 | Swiss Protein Identification Toolbox | 2026-07-25 12:07:25 | 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 | 2026-07-25 12:07:29 | 0 | ||||||||
|
VirVarSeq Resource Report Resource Website 10+ mentions |
VirVarSeq (RRID:SCR_012116) | software resource | Software for a low frequency Virus Variant detection pipeline for Illumina data. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25178459 | OMICS_05534 | SCR_012116 | 2026-07-25 12:07:27 | 11 | |||||||||
|
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 | 2026-07-25 12:07:29 | 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 | 2026-07-25 12:07:29 | 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 | 2026-07-25 12:07:32 | 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 | 2026-07-25 12:07:32 | 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 | Dynamical Hierarchical Agglomerative Clustering | 2026-07-25 12:07:28 | 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 | 2026-07-25 12:07:30 | 81 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the nidm-terms Resources search. From here you can search through a compilation of resources used by nidm-terms and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that nidm-terms has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on nidm-terms then you can log in from here to get additional features in nidm-terms such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into nidm-terms you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
