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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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Primer3 Resource Report Resource Website 10000+ mentions |
Primer3 (RRID:SCR_003139) | Primer3 | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool used to design PCR primers from DNA sequence - often in high-throughput genomics applications. It does everything from mispriming libraries to sequence quality data to the generation of internal oligos. | primer, primer design, polymerase chain reaction, pcr primer, dna sequence, c, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Primer3Plus is related to: Primer-BLAST has parent organization: University of Tartu; Tartu; Estonia |
NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:22730293 PMID:17379693 DOI:10.1385/1-59259-192-2:365 DOI:10.1385/1-59259-192-2:365 |
Free, Freely available | nlx_156833, OMICS_02325, biotools:primer3 | http://bioinfo.ut.ee/primer3-0.4.0/, http://sourceforge.net/projects/primer3/, http://frodo.wi.mit.edu/primer3, https://bio.tools/primer3, https://sources.debian.org/src/primer3/, https://sources.debian.org/src/primer3/ | SCR_003139 | SciCrunch Registry | Primer3web - Pick primers from a DNA sequence, Primer3 - PCR primer design tool, Primer3web | 2026-10-24 12:44:52 | 11934 | ||||
|
GenePattern Resource Report Resource Website 1000+ mentions |
GenePattern (RRID:SCR_003201) | GenePattern | data analysis software, data processing software, software application, software resource | A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. | gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is affiliated with: GenePattern Notebook is related to: TIGRESS has parent organization: Broad Institute |
NCI ; NIGMS |
PMID:16642009 | Free, Freely available | biotools:genepattern, OMICS_01855, nif-0000-30654 | https://bio.tools/genepattern | SCR_003201 | SciCrunch Registry | 2026-10-24 12:44:53 | 1135 | |||||
|
RevMan Resource Report Resource Website 10000+ mentions |
RevMan (RRID:SCR_003581) | RevMan | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00244 | SCR_003581 | SciCrunch Registry | Review Manager | 2026-10-24 12:44:59 | 12962 | ||||||||
|
Scion Image Resource Report Resource Website 5000+ mentions |
Scion Image (RRID:SCR_008673) | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Commercial software vendor. | imaging, industrial, scientific | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33408 | SCR_008673 | SciCrunch Registry | 2026-10-24 12:46:08 | 5759 | |||||||||
|
MACH Resource Report Resource Website 500+ mentions |
MACH (RRID:SCR_009621) | data analysis software, data processing software, software application, software resource | QTL analysis based on imputed dosages/posterior_probabilities. | genetic association, genomic analysis, imaging genomics, snp, gene, quantitative trait analysis, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 DOI:10.1002/gepi.20533 |
Free, Non-commercial, Acknowledgement requested | nlx_155856, biotools:mach | http://www.nitrc.org/projects/mach, https://bio.tools/mach | https://sources.debian.org/src/mach-haplotyper/ | SCR_009621 | SciCrunch Registry | mach2qtl, MaCH | 2026-10-24 12:46:17 | 937 | |||||
|
WEBLOGO Resource Report Resource Website 1000+ mentions |
WEBLOGO (RRID:SCR_010236) | data access protocol, service resource, software resource, web service | Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator. | Generate sequence logo, pattern graphical representation, multiple sequence alignment, sequence logo generator, amino acid sequence alignment, nucleic acid sequence alignment, sequence alignment representation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
NHGRI K22 HG00056; NIGMS P50 GM62412; Searle Scholars program |
PMID:15173120 | Free, Available for download, Freely available | nlx_156853, biotools:weblogo_3 | http://weblogo.threeplusone.com/, https://bio.tools/weblogo_3 | SCR_010236 | SciCrunch Registry | WebLogo Version 2.8.2, WebLogo3, WebLogo | 2026-10-24 12:46:18 | 3980 | |||||
|
ABySS Resource Report Resource Website 500+ mentions |
ABySS (RRID:SCR_010709) | ABySS | data analysis software, data processing software, sequence analysis software, software application, software resource | Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements. | paired-end sequence assembler, short reads, assembling human genome, large genomes, bloom filter, |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
British Columbia Cancer Foundation ; Genome British Columbia ; Genome Canada ; NHGRI R01HG007182 |
PMID:19251739 DOI:10.1101/068338 DOI:10.1101/gr.214346.116 |
Free, Available for download, Freely available | OMICS_00006, biotools:abyss | https://github.com/bcgsc/abyss, https://sources.debian.org/src/abyss/, https://bio.tools/abyss, | SCR_010709 | SciCrunch Registry | ABySS 1.0, ABySS 2.0 | 2026-10-24 12:46:22 | 808 | ||||
|
beadarray Resource Report Resource Website 100+ mentions |
beadarray (RRID:SCR_001314) | beadarray | software resource | Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. | microarray, quality control, one channel, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
PMID:17586828 | GNU General Public License, v2 | OMICS_02021, biotools:beadarray | https://bio.tools/beadarray | SCR_001314 | SciCrunch Registry | beadarray - Quality assessment and low-level analysis for Illumina BeadArray data | 2026-10-24 12:44:29 | 123 | |||||
|
BLASTN Resource Report Resource Website 10000+ mentions |
BLASTN (RRID:SCR_001598) | BLASTn | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast. | nucleotide, alignment, compare, sequence, genome, blast, transcript, dna sequence |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI works with: Seek and Blastn works with: RMBlast |
PMID:17666756 PMID:18567917 |
Free, Freely available | nlx_153932, OMICS_00990 | http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome | SCR_001598 | SciCrunch Registry | NCBI BLASTN, Nucleotide Blast, Standard Nucleotide BLAST | 2026-10-24 12:44:34 | 21160 | |||||
|
Sequencher Resource Report Resource Website 5000+ mentions |
Sequencher (RRID:SCR_001528) | Sequencher sequence analysis software | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for Next-Generation DNA sequencing, Sanger DNA analysis, and RNA sequencing. It contains sequence analysis tools which include reference-guided alignments, de novo assembly, variant calling, and SNP analyses. It has integrated the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data. | dna, sequencing, sequence analysis software, NGS, sanger, data visualization |
is listed by: OMICtools is listed by: SoftCite |
Available for download | OMICS_01817 | http://genecodes.com/sequencher-features | SCR_001528 | SciCrunch Registry | Sequencher sequence analysis software | 2026-10-24 12:44:33 | 5032 | ||||||
|
Jalview Resource Report Resource Website 1000+ mentions |
Jalview (RRID:SCR_006459) | Jalview | software resource | A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. | edit, analysis, annotation, multiple sequence alignment, wysiwyg, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Dundee; Scotland; United Kingdom |
BBSRC BBSB16542 | PMID:19151095 DOI:10.1093/bioinformatics/btp033 |
GNU General Public License, v3, Acknowledgement requested | OMICS_00885, biotools:Jalview | https://bio.tools/Jalview, https://sources.debian.org/src/jalview/ | SCR_006459 | SciCrunch Registry | 2026-10-24 12:45:43 | 4136 | |||||
|
BEDTools Resource Report Resource Website 10000+ mentions |
BEDTools (RRID:SCR_006646) | BEDTools | software resource | A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line. | genomics, bed, sam, bam, overlap, sequencing, intersect, coverage, gff, vcf, bedgraph, interval, genome arithmetic, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Hydra is related to: pybedtools is required by: SL-quant |
PMID:20110278 DOI:10.1093/bioinformatics/btq033 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01159, biotools:bedtools | https://code.google.com/p/bedtools/, https://bio.tools/bedtools, https://sources.debian.org/src/bedtools/ | SCR_006646 | SciCrunch Registry | bedtools - a swiss army knife for genome arithmetic, bedtools: a flexible suite of utilities for comparing genomic features | 2026-10-24 12:45:46 | 11365 | |||||
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geNORM Resource Report Resource Website 5000+ mentions |
geNORM (RRID:SCR_006763) | GENORM | data analysis software, data processing software, software application, software resource | Software to determine most stable reference (housekeeping) genes from set of tested candidate reference genes in given sample panel. From this, gene expression normalization factor can be calculated for each sample based geometric mean of user-defined number of reference genes. | reference gene, quantitative real time pcr |
is used by: RefFinder is listed by: OMICtools is listed by: SoftCite is related to: qBasePLUS has parent organization: Ghent University; Ghent; Belgium |
PMID:19131113 PMID:12519963 |
nlx_156922, OMICS_02316 | http://medgen.ugent.be/~jvdesomp/genorm/ | SCR_006763 | SciCrunch Registry | 2026-10-24 12:45:49 | 5414 | |||||||
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ShortRead Resource Report Resource Website 100+ mentions |
ShortRead (RRID:SCR_006813) | ShortRead | software resource | Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats. | high throughput sequence data, short read, DNA sequences, short read data |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Bioconductor |
PMID:19654119 | Free, Available for download, Freely available | OMICS_01076 | https://sources.debian.org/src/r-bioc-shortread/ | SCR_006813 | SciCrunch Registry | ShortRead - Classes and methods for high-throughput short-read sequencing data. | 2026-10-24 12:45:49 | 235 | |||||
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PLINK Resource Report Resource Website 10000+ mentions Issue |
PLINK (RRID:SCR_001757) | data analysis software, data processing software, software application, software resource, software toolkit | Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software. | gene, genetic, genomic, genotype, phenotype, copy number variant, whole-genome association, population, linkage analysis, whole-genome association study, data management, summary statistics, population stratification, association analysis, identity-by-descent estimation |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Whap is related to: PLINK/SEQ is related to: Haploview is related to: MendelIHT.jl |
PMID:17701901 DOI:10.1086/519795 |
Free, Available for download, Freely Available | nlx_154200, OMICS_00206, SCR_021271 | https://zzz.bwh.harvard.edu/plink/, https://www.cog-genomics.org/plink/1.9/general_usage#cite, https://sources.debian.org/src/plink/ | http://pngu.mgh.harvard.edu/~purcell/plink/ | SCR_001757 | SciCrunch Registry | PLINK 1.9, PLINK/SEQ, plink - Whole genome association analysis toolset | 2026-10-24 12:44:37 | 16581 | |||||
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GenABEL Resource Report Resource Website 500+ mentions |
GenABEL (RRID:SCR_001842) | software library, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits. | r, genome-wide association, single nucleotide polymorphism |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: SoftCite |
Centre for Medical Systems Biology; Netherlands ; Netherlands Genomics Initiative ; Netherlands Organisation for Scientific Research ; Russian Foundation for Basic Research |
PMID:17384015 DOI:10.1186/1471-2105-11-134 DOI:10.1093/bioinformatics/btm108 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154328, OMICS_00234 | http://mga.bionet.nsc.ru/~yurii/ABEL/GenABEL/, https://cran.r-project.org/web/packages/GenABEL/index.html, https://sources.debian.org/src/probabel/ | SCR_001842 | SciCrunch Registry | GenABEL package, R/GENABEL | 2026-10-24 12:44:38 | 506 | |||||
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FreeSurfer Resource Report Resource Website 10000+ mentions |
FreeSurfer (RRID:SCR_001847) | FreeSurfer | data processing software, data visualization software, image analysis software, software application, software resource | Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS. | processing, analysis, human, brain, MRI, image, reconstruction, cortical, surface, fMRI, data |
is used by: Wisconsin Cortical Thickness Analysis (CTA) Toolbox is used by: freesurfR is used by: Automatic Analysis is used by: NHP Freesurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: Debian is listed by: SoftCite is related to: PySurfer is related to: RFT FDR is related to: FMRLAB is related to: TRACULA is related to: BASH4RfMRI has parent organization: Harvard University; Cambridge; United States has plug in: JOSA works with: NIAG Addiction Data |
NCRR RR014075; NCRR U24 RR021382; NINDS R01 NS052585 |
PMID:22248573 | Free, Available for download, Freely available | nif-0000-00304 | https://sources.debian.org/src/freesurfer/, http://www.nitrc.org/projects/freesurfer, http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall | SCR_001847 | SciCrunch Registry | 2026-10-24 12:44:38 | 12664 | |||||
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AStalavista Resource Report Resource Website 50+ mentions |
AStalavista (RRID:SCR_001815) | AStalavista | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool that extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, it detects the variations in their splicing structure and identifies all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. It provides a visual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase, etc. | alternative splicing event, alternative splicing, visualization, genome, transcript |
is listed by: OMICtools is listed by: SoftCite has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:17485470 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01943 | http://genome.imim.es/astalavista, http://genome.crg.es/astalavista/ | SCR_001815 | SciCrunch Registry | Alternative Splicing transcriptional landscape visualization tool | 2026-10-24 12:44:36 | 86 | |||||
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Pathway Commons Resource Report Resource Website 10+ mentions |
Pathway Commons (RRID:SCR_002103) | PC | data access protocol, data or information resource, database, software resource, web service | Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013) | biological pathway, pathway, molecule, biopax, standard exchange format, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: cPath is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: IntAct is related to: Reactome is related to: MINT is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: Cancer Cell Map is related to: HPRD - Human Protein Reference Database is related to: Integrated Molecular Interaction Database is related to: Pathway Interaction Database is related to: CHEBI is related to: UniProt is related to: PANTHER is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit has parent organization: University of Toronto; Ontario; Canada |
NHGRI P41HG004118; NIGMS 2R01GM070743-06; NIGMS 1T32 GM083937; Cancer Biomedical Informatics Grid |
PMID:21071392 | Free, Freely available | nif-0000-20884, r3d100012731, biotools:PathwayCommons_web_service_API | https://bio.tools/PathwayCommons_web_service_API | SCR_002103 | SciCrunch Registry | 2026-10-24 12:44:40 | 14 | |||||
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SAMTOOLS Resource Report Resource Website 10000+ mentions |
SAMTOOLS (RRID:SCR_002105) | SAMtools | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. | Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: ROSE is used by: Fcirc is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SNVer is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Platypus is related to: shovill is related to: pysam has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: SAMtools/BCFtools is required by: RelocaTE is required by: Wessim is required by: SL-quant is required by: smMIPfil |
NHGRI U54 HG002750; Wellcome Trust |
PMID:19505943 PMID:21903627 DOI:10.1093/bioinformatics/btp352 |
Free, Available for download, Freely available | SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 | https://github.com/samtools/samtools, https://github.com/samtools/htslib, https://bio.tools/samtools, https://sources.debian.org/src/samtools/ | http://samtools.sourceforge.net/ | SCR_002105 | SciCrunch Registry | samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools | 2026-10-24 12:44:42 | 33299 |
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