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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.
https://github.com/MRCIEU/PhenoSpD
Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool.
Proper citation: PhenoSpD (RRID:SCR_016359) Copy
http://bioinf.bio.uth.gr/nat-ncs2
Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins.
Proper citation: NAT/NCS2 Hound (RRID:SCR_016473) Copy
https://pan.genomics.cn/ucdisk/s/VjuIRb&code=877833
Pipeline for construction and graphical visualization of annotated pangenome networks from microbial genomes. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data provides pangenome analysis to uncultured microbial taxa., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MetaPGN (RRID:SCR_016472) Copy
http://tools.thermofisher.com/content/sfs/manuals/nd-1000-v3.8-users-manual-8%205x11.pdf
Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution.
Proper citation: Thermo Fisher: Nanodrop 1000 Spectrophotometer (RRID:SCR_016517) Copy
https://deeptools.readthedocs.io/en/develop/
Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches.
Proper citation: Deeptools (RRID:SCR_016366) Copy
https://gitlab.com/vtraver/PNNsMiceMachineVision
Data and code (Python) related to research paper: V. Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera "Cocaine-induced preference conditioning: a machine vision perspective".
Proper citation: PNNsMiceMachineVision (RRID:SCR_016485) Copy
http://www.flywings.org.uk/morphoj_page.htm
Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data.
Proper citation: MorphoJ (RRID:SCR_016483) Copy
https://github.com/sblanck/smagexp
Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more.
Proper citation: SMAGEXP (RRID:SCR_016360) Copy
https://www.ncbi.nlm.nih.gov/biocollections
Registry of bio-collections linked to genomes. Collection of curated dataset of metadata for culture collections, museums, herbaria and other natural history collections, including Darwin Core institution and collection codes, and URL formulae for mapping specimen ids to web pages at the collection site.
Proper citation: NCBI Biocollections (RRID:SCR_016459) Copy
https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf
Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.
Proper citation: 1000 Fungal Genome Project (RRID:SCR_016463) Copy
http://www.nitrc.org/projects/mica/
Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.
Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy
https://github.com/WGS-TB/MentaLiST
Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.
Proper citation: MentaLiST (RRID:SCR_016469) Copy
Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
Proper citation: cisTEM (RRID:SCR_016502) Copy
Portal for lung histochemistry data. For structural and molecular data regarding normal perinatal and postnatal lung development in the mouse and human. For public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology .Contains lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers. Used to serve as a research resource and public education tool.
Proper citation: LungMap (RRID:SCR_016347) Copy
https://www.mrc-lmb.cam.ac.uk/kzhang/Gctf/
Software tool as a Graphics Processing Units (GPU) accelerated computer program for real-time contrast transfer function (CTF) determination and correction. Used for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GCTF (RRID:SCR_016500) Copy
Microbial stock center. Collaborative platform for the pan-European research infrastructure for microbial resources. Provides access to microorganisms, their derivatives, associated data and services for research, development and application.
Proper citation: MIRRI (RRID:SCR_016461) Copy
Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.
Proper citation: Global Catalogue of Microorganisms (RRID:SCR_016460) Copy
https://imaps.genialis.com/iclip
Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions.
Proper citation: iMaps (RRID:SCR_016705) Copy
https://github.com/fbreitwieser/pavian
Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome.
Proper citation: Pavian (RRID:SCR_016679) Copy
https://github.com/tomazc/iCount
Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps.
Proper citation: iCount (RRID:SCR_016712) Copy
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