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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-08-01 12:03:13 | 0 | ||||||
|
seqbias Resource Report Resource Website 10+ mentions |
seqbias (RRID:SCR_006832) | seqbias | software resource | Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
GNU Lesser General Public License | OMICS_01237, biotools:seqbias, BioTools:seqbias | https://bio.tools/seqbias, https://bio.tools/seqbias, https://bio.tools/seqbias | SCR_006832 | seqbias - Estimation of per-position bias in high-throughput sequencing data | 2026-08-01 12:03:13 | 30 | ||||||
|
eDMR Resource Report Resource Website 10+ mentions |
eDMR (RRID:SCR_006960) | eDMR | software resource | Comprehensive differentially methylated regions (DMR) analysis based on bimodal normal distribution model and weighted cost function for regional methylation analysis optimization. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
MIT License | biotools:edmr, OMICS_00622 | https://bio.tools/edmr | SCR_006960 | 2026-08-01 12:03:25 | 19 | |||||||
|
MethylAid Resource Report Resource Website 50+ mentions |
MethylAid (RRID:SCR_002659) | software resource | Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored. | software package, illumina, mac os x, unix/linux, windows, r, dna methylation, gui, methylation array, microarray, quality control, two channel, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:25147358 | Free, Available for download, Freely available | biotools:methylaid, OMICS_05457 | http://www.bioconductor.org/packages/release/bioc/html/MethylAid.html, http://shiny.bioexp.nl/MethylAid/, https://bio.tools/methylaid | SCR_002659 | MethylAid - Visual and interactive quality control of large Illumina 450k data sets, MethylAid: Visual and interactive quality control of large Illumina 450k data sets | 2026-08-01 12:01:52 | 65 | ||||||
|
libmgf Resource Report Resource Website |
libmgf (RRID:SCR_002664) | software resource | A flex/bison-based C++ Mascot Generic Format (MGF) parser library. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20334363 | Free, Available for download, Freely available | OMICS_03343, biotools:libmgf, BioTools:libmgf | https://bio.tools/libmgf, https://bio.tools/libmgf, https://bio.tools/libmgf | SCR_002664 | MGFp, libmgf (formerly MGFp) | 2026-08-01 12:02:12 | 0 | ||||||
|
ExomeDepth Resource Report Resource Website 100+ mentions |
ExomeDepth (RRID:SCR_002663) | software resource | Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. | software package, unix/linux, mac os x, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:22942019 | Free, Available for download, Freely available | OMICS_05443, biotools:exomedepth | https://bio.tools/exomedepth | SCR_002663 | 2026-08-01 12:01:52 | 262 | |||||||
|
libCSAM Resource Report Resource Website 1+ mentions |
libCSAM (RRID:SCR_002766) | software resource | Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24728856 | Free, Freely available, Available for download | OMICS_03750, biotools:libcsam | https://bio.tools/libcsam | SCR_002766 | 2026-08-01 12:02:16 | 1 | |||||||
|
RopeBWT2 Resource Report Resource Website 10+ mentions |
RopeBWT2 (RRID:SCR_002673) | software resource | A software tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of BCR and dynamic FM-index. Nonetheless, ropeBWT2 is unique in that it may implicitly sort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Burrows-Wheeler transform |
PMID:25107872 | Free, Available for download, Freely available | biotools:ropebwt2, OMICS_05300 | https://bio.tools/ropebwt2 | SCR_002673 | 2026-08-01 12:02:13 | 11 | |||||||
|
NetPathMiner Resource Report Resource Website 1+ mentions |
NetPathMiner (RRID:SCR_002757) | software resource | Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths. | software package, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25075120 | Free, Freely available, Available for download | biotools:netpathminer, OMICS_05210 | https://bio.tools/netpathminer | SCR_002757 | NetPathMiner: R package for network path mining through gene expression | 2026-08-01 12:01:54 | 3 | ||||||
|
GATE Resource Report Resource Website 100+ mentions |
GATE (RRID:SCR_002756) | data analysis resource | Model-based, open source software analysis tool for chromatin states prediction based on time-course epigenetic marks data. It uses a combinatory Finite Mixture model nested with HMM to model the time course marks data in which each single hidden markov model describes the hidden states for a region set across different time points. | chromatin state prediction software, time course epigenetic data, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23033340 | Free, Freely available, Available for download | OMICS_03065, biotools:gate | https://github.com/yu68/GATE, https://bio.tools/gate | SCR_002756 | Genomic Annotation from Time-couse Epigenomic data, Genomic Annotation from Time-couse Epigenomic data (GATE) | 2026-08-01 12:02:16 | 317 | ||||||
|
pNovo+ Resource Report Resource Website 1+ mentions |
pNovo+ (RRID:SCR_002860) | software resource | A de novo peptide sequencing algorithm using complementary higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) tandem mass spectra. | mass spectrometry, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:23272783 | Free, Freely available | biotools.pNovo_3, OMICS_02470 | https://bio.tools/pNovo_3 | SCR_002860 | 2026-08-01 12:01:57 | 7 | |||||||
|
pairheatmap Resource Report Resource Website |
pairheatmap (RRID:SCR_003109) | software resource | A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:24016862 | Free, Available for download, Freely available | biotools:pairheatmap, OMICS_04853 | https://www.rdocumentation.org/packages/pairheatmap/versions/1.0.1/topics/pairheatmap | SCR_003109 | pairheatmap: A tool for comparing heatmaps | 2026-08-01 12:02:02 | 0 | ||||||
|
MFEprimer Resource Report Resource Website 10+ mentions |
MFEprimer (RRID:SCR_003066) | software resource | A fast thermodynamics-based software program for checking PCR primer specificity against genomic DNA and mRNA/cDNA sequence databases. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22689644 | Free, Available for download, Freely available | biotools:mfeprimer-2.0, OMICS_02355 | https://www.mfeprimer.com/ | SCR_003066 | MFEprimer-2.0 | 2026-08-01 12:02:01 | 19 | ||||||
|
eQtlBma Resource Report Resource Website 1+ mentions |
eQtlBma (RRID:SCR_003102) | software resource | Software package that implements Bayesian statistical methods to detect eQTLs jointly in multiple subgroups (e.g. tissues). Key features are to borrow information across subgroups, to explicitly model heterogeneity (qualitatively and quantitatively), and to borrow information across genes to estimate hyper-parameters from the data (empirical Bayes). | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
PMID:23671422 | Free, Available for download, Freely available | biotools:eqtlbma, OMICS_04875 | https://bio.tools/eqtlbma | SCR_003102 | 2026-08-01 12:02:26 | 5 | |||||||
|
Triplex Resource Report Resource Website 10+ mentions |
Triplex (RRID:SCR_003061) | software resource | Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D. | software package, mac os x, unix/linux, windows, r, gene regulation, sequence matching, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23709494 | Free, Available for download, Freely available | OMICS_06259, biotools:triplex | http://www.fi.muni.cz/~lexa/triplex/, https://bio.tools/triplex | SCR_003061 | triplex - Search and visualize intramolecular triplex-forming sequences in DNA | 2026-08-01 12:02:25 | 10 | ||||||
|
bwtool Resource Report Resource Website 10+ mentions |
bwtool (RRID:SCR_003035) | software resource | A command-line utility for bigWig files designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Its functionality is subdivided into subprograms that roughly fall into three categories: data extraction, analysis, and data modification, although e.g. in the case of the matrix program or the sax program, the boundary between data extraction and analysis isn't very strong. The data modification programs all have the behavior that a bigWig is inputted and a new bigWig is outputted. | standalone software, unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:2448936 | Free, Available for download, Freely available | biotools:bwtool, OMICS_05125 | https://bio.tools/bwtool | SCR_003035 | 2026-08-01 12:02:00 | 21 | |||||||
|
SMRT View Resource Report Resource Website 1+ mentions |
SMRT View (RRID:SCR_003029) | software resource | An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results. | standalone software, unix/linux, mac os x, windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:smrt_view, OMICS_05137 | https://bio.tools/smrt_view | SCR_003029 | SMRT-View | 2026-08-01 12:02:24 | 9 | |||||||
|
ProRata Resource Report Resource Website 1+ mentions |
ProRata (RRID:SCR_002988) | software resource | A quantitative proteomics software program for accurate protein abundance ratio estimation with confidence interval evaluation. | standalone software, mass spectrometry, proteomics, stable isotope labeling, quantitative proteomics, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:17037911 | GNU General Public License, v3 | biotools:prorata, OMICS_02502 | https://bio.tools/prorata | SCR_002988 | ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation, prorata - Quantitative Proteomics Software | 2026-08-01 12:01:59 | 9 | ||||||
|
rbsurv Resource Report Resource Website 1+ mentions |
rbsurv (RRID:SCR_001175) | rbsurv | software resource | Software package that selects genes associated with survival. | microarray, gene, survival, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:rbsurv, BioTools:rbsurv, OMICS_02088 | https://bio.tools/rbsurv, https://bio.tools/rbsurv, https://bio.tools/rbsurv | SCR_001175 | rbsurv - Robust likelihood-based survival modeling with microarray data | 2026-08-01 12:01:24 | 1 | ||||||
|
Sherman Resource Report Resource Website 100+ mentions |
Sherman (RRID:SCR_001294) | Sherman | software resource | Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments. | perl, bisulfite sequencing, high-throughput sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute |
Free, Available for download, Freely available | biotools:sherman, OMICS_02041 | http://www.bioinformatics.babraham.ac.uk/projects/sherman/ | SCR_001294 | Sherman - bisulfite-treated Read FastQ Simulator | 2026-08-01 12:01:37 | 122 |
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