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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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BRB-ArrayTools Resource Report Resource Website 500+ mentions |
BRB-ArrayTools (RRID:SCR_010938) | BRB-ArrayTools | software resource | An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00750, biotools:brb-arraytools | https://bio.tools/brb-arraytools | SCR_010938 | SciCrunch Registry | 2026-11-07 11:57:19 | 573 | |||||||
|
BWA Resource Report Resource Website 1000+ mentions |
BWA (RRID:SCR_010910) | BWA | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp. | sequence, alignment, reference, genome, human, short, long, read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill is related to: Proovread is related to: BWA-MEM2 has parent organization: SourceForge is required by: RelocaTE |
PMID:19451168 PMID:20080505 DOI:10.1093/bioinformatics/btp324 |
Free, Available for download, Freely available | SCR_015853, biotools:bwa-sw, OMICS_00654 | https://sourceforge.net/projects/bio-bwa/files/, https://bio.tools/bwa-sw, https://sources.debian.org/src/bwa/ | SCR_010910 | SciCrunch Registry | Burrows-Wheeler Aligner (BWA), Burrows-Wheeler Aligner | 2026-11-07 11:57:07 | 2638 | |||||
|
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 | 2026-11-07 11:54:28 | 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 | 2026-11-07 11:54:20 | 5032 | ||||||
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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 | 2026-11-07 11:54:33 | 16581 | |||||
|
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 | 2026-11-07 11:54:34 | 506 | |||||
|
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 | 2026-11-07 11:54:34 | 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 | 2026-11-07 11:54:42 | 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 | 2026-11-07 11:54:51 | 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 | 2026-11-07 11:54:37 | 33299 | |||
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Fiji Resource Report Resource Website 10000+ mentions |
Fiji (RRID:SCR_002285) | Fiji | data processing software, image processing software, software application, software resource, source code | Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences. | imaging, microscopy, windows, linux, java, mac osx, bio.tools |
uses: Fiji/ImageJ is used by: MuscleJ is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: ImageJ is related to: SynapseLocator is related to: Golddigger is related to: Analyze Spheroid Cell Invasion In 3D Matrix has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany has plug in: BioVoxxel Toolbox has plug in: imctools has plug in: Big Data Processor has plug in: Sholl Analysis has plug in: SAIBR has plug in: TWOMBLI |
PMID:22743772 | Free, Available for download, Freely available, Acknowledgement requested | SciRes_000137, biotools:Fiji | https://github.com/fiji/fiji, https://bio.tools/Fiji | SCR_002285 | SciCrunch Registry | Fiji is just ImageJ | 2026-11-07 11:54:45 | 40972 | |||||
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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 | 2026-11-07 11:55:53 | 4136 | |||||
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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 | 2026-11-07 11:55:58 | 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 | 2026-11-07 11:56:14 | 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. | 2026-11-07 11:56:02 | 235 | |||||
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JCB DataViewer Resource Report Resource Website 10+ mentions |
JCB DataViewer (RRID:SCR_002633) | JCB DataViewer | data or information resource, data repository, database, image repository, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots. | microscopy, standardization, data sharing, archiving, data management, metadata standard, visualization, analysis, image collection, histology, electron micrograph, digital scan, gel, blot |
is listed by: FORCE11 is listed by: SoftCite is related to: OME-TIFF Format has parent organization: Rockefeller University; New York; USA |
Glencoe Software ; OME - Open Microscopy Environment |
PMID:22869591 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156057, r3d100010895 | https://doi.org/10.17616/R3PW4G | SCR_002633 | SciCrunch Registry | 2026-11-07 11:54:43 | 14 | |||||
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FSL Resource Report Resource Website 5000+ mentions |
FSL (RRID:SCR_002823) | software library, software resource, software toolkit | Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas. | dti, brain, imaging, data, structural, mri, diffusion, function, preprocessing, analysis, statistical, tractography, atlas, neuroimaging, parameter, reconstruction, volumetric, segmentation, independent, component, temporal, transformation |
uses: Neuroimaging Data Model is used by: Spinal Cord Toolbox is used by: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) is used by: XFSL: An FSL toolbox is used by: CMIND PY lists: SUSAN lists: FUGUE lists: Miscvis lists: BayCEST lists: ICA-PNM is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Rodent Brain Extraction Tool is related to: Human Connectome Coordination Facility is related to: BASH4RfMRI is related to: DW-MRI registration in FSL is related to: FSL extensions is related to: Diffusion MRI of Traumatic Brain Injury is related to: Segmentation of Hippocampus Subfields is related to: masked ICA (mICA) Toolbox has parent organization: University of Oxford; Oxford; United Kingdom has plug in: Multivariate Exploratory Linear Optimized Decomposition into Independent Components has plug in: FMRI Expert Analysis Tool has plug in: FABBER has plug in: BASIL has plug in: VERBENA has plug in: Brain Extraction Tool has plug in: FMRIB's Automated Segmentation Tool has plug in: FMRIB’s Integrated Registration and Segmentation Tool has plug in: Harvard - Oxford Cortical Structural Atlas has plug in: FMRIB's Linear Image Registration Tool has plug in: FNIRT has plug in: FSLVBM has plug in: SIENA has plug in: SIENAX has plug in: Multimodal Image Segmentation Tool has plug in: Brain Intensity AbNormality Classification Algorithm has plug in: Multimodal Surface Matching has plug in: fsl_anat has plug in: FMRIB's Diffusion Toolbox has plug in: Tract Based Spatial Statistics has plug in: XTRACT has plug in: eddy has plug in: topup has plug in: eddyqc has plug in: randomise has plug in: PALM has plug in: fsl-cluster has plug in: FDR has plug in: DualRegression has plug in: FLOBS has plug in: FSLeyes has plug in: Fslutils has plug in: Atlasquery has plug in: MCFLIRT has plug in: POSSUM has plug in: FSL-MRS |
BBSRC ; EPSRC ; GlaxoSmithKline ; MRC ; Pfizer |
PMID:21979382 PMID:19059349 PMID:15501092 |
Free, Available for download, Freely available | nif-0000-00305, SCR_007368, birnlex_2067 | http://www.nitrc.org/projects/fsl, http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/, https://sources.debian.org/src/fsl/ | SCR_002823 | SciCrunch Registry | , FMRIB Software Library, fMRIB Software Library, Functional Magnetic Resonance Imaging of the Brain Software Library | 2026-11-07 11:54:46 | 5015 | |||||
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Primer3Plus Resource Report Resource Website 1000+ mentions |
Primer3Plus (RRID:SCR_003081) | Primer3Plus | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. | primer, dna sequence, primer design, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Primer3 has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
Howard Hughes Medical Institute ; NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:17485472 | Free, Freely available | biotools:primer3plus, OMICS_02347 | https://bio.tools/primer3plus | SCR_003081 | SciCrunch Registry | Primer3Plus - pick primers from a DNA sequence | 2026-11-07 11:55:02 | 1860 | ||||
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DIALIGN Resource Report Resource Website 10+ mentions |
DIALIGN (RRID:SCR_003041) | DIALIGN | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/ | dna, protein, sequence alignment, sequence, alignment, fasta, genome, genomic sequence, homology, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15215344 PMID:23620293 DOI:10.1186/1748-7188-3-6 |
Free, Available for download, Freely available | nif-0000-30417, OMICS_24606, OMICS_00973, biotools:dialign-tx | http://dialign.gobics.de/, https://bio.tools/dialign-tx | https://sources.debian.org/src/dialign-tx/ | SCR_003041 | SciCrunch Registry | DIALIGN at GOBICS | 2026-11-07 11:55:06 | 44 | ||||
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RStudio Resource Report Resource Website 1000+ mentions |
RStudio (RRID:SCR_000432) | RStudio | software resource | Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux). | R, statistical, computing, environment |
is used by: PlotsOfData is listed by: Debian is listed by: SoftCite is related to: rSPRITE is related to: shinyCircoss is parent organization of: Shiny is required by: circlncRNAnet |
Restricted | SciRes_000113 | https://sources.debian.org/src/rstudio/, https://posit.co/download/rstudio-desktop/ | http://www.rstudio.com/ | SCR_000432 | SciCrunch Registry | 2026-11-07 11:54:03 | 1191 |
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