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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-02-14 02:02:37 | 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 | 2026-02-14 02:02:37 | 81 | ||||||||
|
Next-gen Sequencing Scaffolding Tool Resource Report Resource Website |
Next-gen Sequencing Scaffolding Tool (RRID:SCR_006762) | Next-gen Sequencing Scaffolding Tool | software resource | Software that implements a greedy algorithm and uses graph theory to link and orient assembled existing contigs quickly and accurately using mate pair information. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00040 | SCR_006762 | 2026-02-14 02:01:23 | 0 | ||||||||||
|
QUASR Resource Report Resource Website 100+ mentions |
QUASR (RRID:SCR_006820) | QUASR | software resource | A lightweight software pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal, demultiplexing, primer-removal, quality-assurance (QA) graphing, quality control (QC), consensus-generation, minority-variant determination, minority-variant graphing. | next generation sequencing, python3, java |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01072 | SCR_006820 | QUASR - Cross-platform NGS processing and analysis pipeline in Python | 2026-02-14 02:01:14 | 213 | |||||||
|
simhtsd Resource Report Resource Website |
simhtsd (RRID:SCR_006822) | simhtsd | software resource | Software that given a reference sequence, will create a large set of short nucleotide reads, simulating the output from today''s high-throughput DNA sequencers, such as the Illumina Genome Analyzer II. | command-line, perl |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2, v3 | OMICS_00256 | SCR_006822 | Simulate High-Throughput Sequencing Data | 2026-02-14 02:01:16 | 0 | |||||||
|
Virmid Resource Report Resource Website 1+ mentions |
Virmid (RRID:SCR_006780) | Virmid | software resource | A Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha). The important features of Virmid are: * Estimation of accurate proporation of control sample in a (mixed) disease sample * Improved SNP and somatic mutation calling with regard to the estimated proportion | somatic mutation, sample impurity, java, snp, variant, disease, control |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at San Diego; California; USA |
PMID:23987214 | OMICS_00095 | SCR_006780 | Virtual Microdissection for SNP calling | 2026-02-14 02:01:15 | 6 | |||||||
|
BIGpre Resource Report Resource Website |
BIGpre (RRID:SCR_006781) | BIGpre | software resource | A quality assessment software package for next-genomics sequencing data. | next generation sequencing, genomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22289480 | GNU General Public License, v3 | biotools:bigpre, OMICS_01035 | https://bio.tools/bigpre | SCR_006781 | 2026-02-14 02:01:23 | 0 | ||||||
|
TaxoAssignement Resource Report Resource Website 100+ mentions |
TaxoAssignement (RRID:SCR_006814) | TANGO | software resource | Software tool for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy. | next generation sequencing, taxonomy, perl |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Polytechnic University of Catalonia; Barcelona; Spain |
MIT License | OMICS_01439 | http://www.cs.upc.edu/~valiente/tango/ | SCR_006814 | Taxonomic assignment of sequences, TANGO: Taxonomic Assignment in Metagenomics | 2026-02-14 02:01:13 | 246 | ||||||
|
GARM Resource Report Resource Website 10+ mentions |
GARM (RRID:SCR_006731) | GARM | software resource | A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01420 | SCR_006731 | Genome Assembler Reconcilation and Merging | 2026-02-14 02:01:22 | 11 | |||||||||
|
PowerMap Resource Report Resource Website 1+ mentions |
PowerMap (RRID:SCR_006721) | PowerMap | software resource | Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support. | neuroimaging, statistical analyses, false discovery rate, 3d spatial image, power calculation, sample size |
has parent organization: Wake Forest School of Medicine; North Carolina; USA has parent organization: SourceForge |
NINDS NS059793 | PMID:22644868 | Free, Public | nlx_152808 | SCR_006721 | 2026-02-14 02:01:14 | 3 | ||||||
|
Samscope Resource Report Resource Website |
Samscope (RRID:SCR_006715) | Samscope | software resource | A lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun! Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments. | c++, visualization, opengl, next generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
GNU Affero General Public License | OMICS_00892 | SCR_006715 | samscope - A lightweight OpenGL SAM/BAM viewer | 2026-02-14 02:01:22 | 0 | |||||||
|
DMEAS Resource Report Resource Website 1+ mentions |
DMEAS (RRID:SCR_006679) | DMEAS | software resource | A user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data. | c# |
is listed by: OMICtools has parent organization: SourceForge |
Creative Commons Attribution License | OMICS_00598 | SCR_006679 | DNA Methylation Entropy Analysis Software, DMEAS - DNA Methylation Entropy Analysis Software | 2026-02-14 02:01:13 | 1 | |||||||
|
HIA Resource Report Resource Website |
HIA (RRID:SCR_006865) | HIA | software resource | A sequence alignment tool to align both short and long reads to a reference genome. HIA has two indexes, a hash table index and a suffix array index. The hash table is capable of the direct lookup of a q-gram and the suffix array is very fast in the lookup of a variable length q-gram. Our experiments show that the hybrid of hash table and suffix array is useful at the perspective of speed to map NGS sequencing reads to a reference genome sequence. | matlab, java, command-line |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00666 | SCR_006865 | Hybrid Index based sequence Alignment, HIA - Hybrid Index based sequence Alignment | 2026-02-14 02:01:14 | 0 | ||||||||
|
fitGCP Resource Report Resource Website |
fitGCP (RRID:SCR_006741) | fitGCP | software resource | Software providing a framework for fitting mixtures of probability distributions to genome coverage profiles. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23589648 DOI:10.1093/bioinformatics/btt147 |
BSD License | OMICS_01046 | https://sources.debian.org/src/fitgcp/ | SCR_006741 | fitGCP - Fitting genome coverage distributions with mixture models | 2026-02-14 02:01:21 | 0 | ||||||
|
GASiC Resource Report Resource Website 1+ mentions |
GASiC (RRID:SCR_006765) | GASiC | software resource | A method to correct read alignment results for the ambiguities imposed by similarities of genomes. | metagenome, genome, sequence, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:22941661 DOI:10.1093/nar/gks803 |
BSD License | OMICS_01437 | https://sources.debian.org/src/gasic/ | SCR_006765 | GASiC - Genome Abundance Similarity Correction, Genome Abundance Similarity Correction | 2026-02-14 02:01:15 | 3 | |||||
|
mrFAST Resource Report Resource Website 10+ mentions |
mrFAST (RRID:SCR_005487) | mrFAST | software resource | Software designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient mannerl. Currently Supported Features: * Output in SAM format * Indels up to 8 bp (4 bp deletions and 4 bp insertions) * Paired-end mapping ** Discordant option to generate mapping file ready for VariationHunter to detect structural variants. * One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq * Matepair library mapping (long inserts with RF orientation). Planned Features: * Multithreading | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SPLITREAD has parent organization: SourceForge |
PMID:19718026 | biotools:mrfast, OMICS_00671 | https://bio.tools/mrfast | SCR_005487 | mrFAST - Micro Read Fast Alignment Search Tool, Micro Read Fast Alignment Search Tool | 2026-02-14 02:00:54 | 16 | ||||||
|
CUSHAW2-GPU Resource Report Resource Website |
CUSHAW2-GPU (RRID:SCR_005480) | CUSHAW2-GPU | software resource | Software program (based on CUSHAW2) designed and optimized for Kepler-based GPUs, but still workable on earlier-generation Fermi-based ones. | c++, genome, alignment |
is listed by: OMICtools is related to: CUSHAW has parent organization: SourceForge |
Apache License | OMICS_00659 | SCR_005480 | 2026-02-14 02:01:08 | 0 | ||||||||
|
CUSHAW Resource Report Resource Website 1+ mentions |
CUSHAW (RRID:SCR_005479) | CUSHAW | software resource | Software package for next-generation sequencing read alignment that is fast and parallel gapped read alignment to large genomes, such as the human genome. | next-generation sequencing, read alignment, genome, alignment |
is listed by: OMICtools is related to: CUSHAW2-GPU has parent organization: Johannes Gutenberg University Mainz; Rhineland-Palatinate; Germany has parent organization: SourceForge |
PMID:22576173 PMID:24466273 |
OMICS_00658 | SCR_005479 | CUSHAW2, CUSHAW3 | 2026-02-14 02:00:56 | 2 | |||||||
|
NGSView Resource Report Resource Website 1+ mentions |
NGSView (RRID:SCR_005637) | NGSView | software resource | A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. | next-generation sequence, alignment, edit, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Acknowledgement requested | biotools:ngsview, OMICS_00891 | https://bio.tools/ngsview | SCR_005637 | 2026-02-14 02:00:58 | 2 | |||||||
|
SAMtools Text Alignment Viewer Resource Report Resource Website 1+ mentions |
SAMtools Text Alignment Viewer (RRID:SCR_005611) | SAMtools tview | software resource | Text alignment viewer software based on the GNU ncurses library that works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice. | text alignment, viewer, maq consensus, indel |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00893 | SCR_005611 | Text Alignment Viewer | 2026-02-14 02:00:56 | 1 |
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
Email: info_at_ dknet.org
