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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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
AMS Resource Report Resource Website |
AMS (RRID:SCR_012140) | software resource | Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22555647 | Apache License | OMICS_05934, biotools:ams | https://bio.tools/ams | SCR_012140 | SciCrunch Registry | AutoMotif Service | 2026-11-07 11:57:40 | 0 | ||||||
|
PhosphoSiteAnalyzer Resource Report Resource Website |
PhosphoSiteAnalyzer (RRID:SCR_012142) | software resource | A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22471441 | Free, Public | biotools:phosphositeanalyzer, OMICS_05951 | https://bio.tools/phosphositeanalyzer | SCR_012142 | SciCrunch Registry | 2026-11-07 11:57:26 | 0 | |||||||
|
DNAcopy Resource Report Resource Website 100+ mentions |
DNAcopy (RRID:SCR_012560) | DNAcopy | software resource | Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
OMICS_00720, biotools:dnacopy | https://bio.tools/dnacopy, https://sources.debian.org/src/r-bioc-dnacopy/ | SCR_012560 | SciCrunch Registry | 2026-11-07 11:57:33 | 349 | ||||||||
|
AutoDock Resource Report Resource Website 10000+ mentions |
AutoDock (RRID:SCR_012746) | autodock | software resource | Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids. | Small molecules receptor binding, automated docking tools, 3D structure, AutoDock 4, AutoDock Vina, ligand, docking |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Autogrid |
PMID:19399780 | Free, Available for download, Freely available | OMICS_01594, biotools:autodock | https://bio.tools/autodock, https://sources.debian.org/src/autodock/ | SCR_012746 | SciCrunch Registry | 2026-11-07 11:57:50 | 13612 | ||||||
|
DEXSeq Resource Report Resource Website 500+ mentions |
DEXSeq (RRID:SCR_012823) | DEXSeq | software resource | Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
OMICS_01329, biotools:dexseq | https://bio.tools/dexseq | SCR_012823 | SciCrunch Registry | 2026-11-07 11:57:31 | 540 | ||||||||
|
edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | data analysis software, data processing software, software application, software resource | Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. | empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SARTools is related to: Bioconductor works with: tximport |
Harris and IBS Honours scholarships ; Independent Research Institutes Infrastructure Support Scheme 361646; Melbourne International Research Scholarship ; NHMRC 406657; Victorian State Government OIS grant |
PMID:19910308 DOI:10.1093/bioinformatics/btp616 |
Free, Available for download, Freely available | OMICS_01308, biotools:edger | https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ | SCR_012802 | SciCrunch Registry | edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R | 2026-11-07 11:57:36 | 23868 | ||||
|
DNaseR Resource Report Resource Website |
DNaseR (RRID:SCR_012819) | DNaseR | software resource | A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:23118738 | Free | biotools:dnaser, OMICS_00517 | https://bio.tools/dnaser | SCR_012819 | SciCrunch Registry | DNaseR: DNase I footprinting analysis of DNase-seq data | 2026-11-07 11:57:39 | 0 | |||||
|
IMGT - the international ImMunoGeneTics information system Resource Report Resource Website 500+ mentions |
IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) | IMGT | analysis service resource, data analysis service, data or information resource, database, portal, production service resource, service resource, topical portal | A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools. | immunogenetics, immunoinformatics, immunoglobulin, antibody, t cell receptor, major histocompatibility complex, immunoglobulin superfamily, major histocompatibility complex superfamily, protein, immune system, sequence, genome, structure, monoclonal antibody, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IMGT Repertoire has parent organization: Montpellier 2 University; Montpellier; France is parent organization of: IMGT/LIGM-DB is parent organization of: IMGT/GENE-DB is parent organization of: IMGT-ONTOLOGY is parent organization of: IMGT/V-QUEST is parent organization of: IMGT/HLA |
CNRS ; MESR ; Reseau National des Genopoles ; Region Languedoc-Roussillon ; European Union BIOMED1 BIOCT930038; European Union Biotechnology BIOTECH2 BIO4CT960037; European Union 5th PCRDT Quality of Life and Management of Living Resources QLG2-2000-01287; Agence Nationale de la recherche ANR BIOSYS06_135457; EU ImmunoGrid IST-028069 |
PMID:18978023 | nif-0000-03011, biotools:imgt | https://bio.tools/imgt | http://imgt.cines.fr | SCR_012780 | SciCrunch Registry | ImMunoGeneTics Information System, IMGT/LIGM, ImMunoGeneTics | 2026-11-07 11:57:38 | 779 | ||||
|
BEDOPS Resource Report Resource Website 100+ mentions |
BEDOPS (RRID:SCR_012865) | BEDOPS | software resource | A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets. |
is listed by: OMICtools is listed by: Debian |
PMID:22576172 DOI:10.1093/bioinformatics/bts277 |
GNU General Public License, v3 | OMICS_00949 | https://sources.debian.org/src/bedops/ | SCR_012865 | SciCrunch Registry | BEDOPS: high-performance genomic feature operations | 2026-11-07 11:57:32 | 237 | ||||||
|
featureCounts Resource Report Resource Website 10000+ mentions |
featureCounts (RRID:SCR_012919) | featureCounts | software resource | A read summarization program, which counts mapped reads for the genomic features such as genes and exons. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is required by: SL-quant |
PMID:24227677 | biotools:featurecounts, OMICS_01160 | https://bio.tools/featurecounts | SCR_012919 | SciCrunch Registry | featureCounts: a universal read summarization program | 2026-11-07 11:57:40 | 14312 | ||||||
|
CloudAligner Resource Report Resource Website 1+ mentions |
CloudAligner (RRID:SCR_012962) | CloudAligner | software resource | A map/reduce based application for mapping short reads generated by the next-generation sequencing machines. | matlab, mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21645377 | GNU General Public License, v3 | OMICS_00656, biotools:cloudaligner | https://bio.tools/cloudaligner | SCR_012962 | SciCrunch Registry | 2026-11-07 11:57:56 | 4 | ||||||
|
NGSmethDB Resource Report Resource Website 1+ mentions |
NGSmethDB (RRID:SCR_012847) | NGSmethDB | data or information resource, data repository, database, service resource, storage service resource | A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20965971 | OMICS_01844, biotools:ngsmethdb | https://bio.tools/ngsmethdb | SCR_012847 | SciCrunch Registry | NGSmethDB - A database for NGS single-cytosine-resolution DNA methylation data | 2026-11-07 11:57:52 | 9 | ||||||
|
MitoBreak Resource Report Resource Website 10+ mentions |
MitoBreak (RRID:SCR_012949) | MitoBreak | data or information resource, data repository, database, service resource, storage service resource | Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements. | mitochondrial dna rearrangement, mitochondrial dna, deletion, duplication, linear, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24170808 | Free, The community can contribute to this resource | biotools:mitobreak, OMICS_01640 | https://bio.tools/mitobreak | SCR_012949 | SciCrunch Registry | 2026-11-07 11:57:55 | 11 | ||||||
|
minfi Resource Report Resource Website 100+ mentions |
minfi (RRID:SCR_012830) | minfi | data analysis software, data processing software, data visualization software, software application, software resource | Software tools for analyzing and visualizing Illumina''s 450k array data. | Illumina, array data, Analyze Illumina Infinium DNA methylation arrays, DNA methylation array, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SWAN has parent organization: Bioconductor |
PMID:28035024 | Free, Available for download, Freely available | biotools:minfi, OMICS_00799, BioTools:minfi | https://bio.tools/minfi, https://bio.tools/minfi, https://bio.tools/minfi | SCR_012830 | SciCrunch Registry | 2026-11-07 11:57:31 | 417 | ||||||
|
RepeatMasker Resource Report Resource Website 10000+ mentions |
RepeatMasker (RRID:SCR_012954) | software resource | Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ). |
uses: Repbase uses: RMBlast is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
DOI:10.1007/978-1-61779-603-6_2 | nlx_156840, OMICS_09436 | https://sources.debian.org/src/repeatmasker/ | SCR_012954 | SciCrunch Registry | repeatmasker.org | 2026-11-07 11:57:41 | 10730 | ||||||||
|
affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | data analysis software, data processing software, software application, software resource | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | SciCrunch Registry | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-11-07 11:57:39 | 3073 | ||||
|
Acacia Resource Report Resource Website 100+ mentions |
Acacia (RRID:SCR_012896) | Acacia | software resource | Accurate error-correction of amplicon pyrosequences. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
DOI:10.1038/nmeth.1990 | OMICS_01116 | https://sources.debian.org/src/acacia/ | SCR_012896 | SciCrunch Registry | 2026-11-07 11:57:40 | 109 | ||||||||
|
charm Resource Report Resource Website 50+ mentions |
charm (RRID:SCR_012992) | charm | software resource | Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
biotools:charm, OMICS_00792 | https://bio.tools/charm | SCR_012992 | SciCrunch Registry | 2026-11-07 11:57:34 | 68 | ||||||||
|
Trinity Resource Report Resource Website 10000+ mentions |
Trinity (RRID:SCR_013048) | Trinity | software resource | Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Broad Institute has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
DOI:10.1038/nbt.1883 | biotools:trinity, OMICS_01327 | https://bio.tools/trinity, https://sources.debian.org/src/trinityrnaseq/ | SCR_013048 | SciCrunch Registry | 2026-11-07 11:57:42 | 10043 | |||||||
|
MethylCoder Resource Report Resource Website 1+ mentions |
MethylCoder (RRID:SCR_012997) | MethylCoder | software resource | A single program that takes of bisulfite-treated reads and outputs per-base methylation data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21724594 | biotools:methylcoder, OMICS_00585 | https://bio.tools/methylcoder | SCR_012997 | SciCrunch Registry | 2026-11-07 11:57:42 | 4 |
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