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http://www.lirmed.com/tam2/

Web server for miRNA set enrichment analysis. TAM 2.0 is updated version of this web server. Allows to test functional and disease annotations of miRNAs by overrepresentation analysis and to compare input de-regulated miRNAs with those de-regulated in other disease conditions via correlation analysis.

Proper citation: TAM (RRID:SCR_023800) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/miRBaseConverter/

Software R package for converting and retrieving information of miRNAs in different miRBase versions. Used for converting and retrieving miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. Can process huge number of miRNAs in short time without other depends.

Proper citation: miRBaseConverter (RRID:SCR_023873) Copy   

•   Source: SciCrunch Registry

http://www.rna-society.org/rnalocate/

Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation.

Proper citation: RNALocate (RRID:SCR_024418) Copy   

•   Source: SciCrunch Registry

https://github.com/BGI-shenzhen/PopLDdecay

Software tool for linkage disequilibrium decay analysis based on variant call format files.

Proper citation: PopLDdecay (RRID:SCR_022509) Copy   

•   Source: SciCrunch Registry

http://lilab-ecust.cn/pharmmapper/index.html

Web server for potential drug target identification using pharmacophore mapping approach.Designed to identify potential target candidates for given probe small molecules including drugs, natural products, or other newly discovered compounds with binding targets unidentified using pharmacophore mapping approach. Used for potential drug target identification with comprehensive target pharmacophore database.

Proper citation: PharmMapper (RRID:SCR_022604) Copy   

•   Source: SciCrunch Registry

https://github.com/basehc/IPEV

Software tool to identify of Prokaryotic and Eukaryotic virus derived sequences in virome using deep learning. Used to calculate set of scores that reflect probability that input sequence fragments are prokaryotic and eukaryotic viral sequences.

Proper citation: IPEV (RRID:SCR_023702) Copy   

•   Source: SciCrunch Registry

http://hdock.phys.hust.edu.cn/

Web server for protein-protein and protein-DNA/RNA docking based on hybrid strategy. With input information for receptor and ligand molecules either amino acid sequences or Protein Data Bank structures, the server automatically predicts their interaction through hybrid algorithm of template-based and template-free docking.

Proper citation: HDOCK server (RRID:SCR_024799) Copy   

•   Source: SciCrunch Registry

http://predict.phasep.pro/

Web server as meta-predictor for phase-separating proteins. Displays proteome-level quantiles of different features, thus profiling PS propensity and providing crucial information for identification of candidate proteins.

Proper citation: PhaSePred (RRID:SCR_024969) Copy   

•   Source: SciCrunch Registry

http://www.atcgn.com:8080/quarTeT/home.html

Web toolkit for studies of large scale T2T genomes. Collection of tools designed for T2T genome assembly and characterization, including reference guided genome assembly, ultra long sequence based gap filling, telomere identification, and de novo centromere prediction. Includes four modules: AssemblyMapper, GapFiller, TeloExplorer, and CentroMiner. Modules can be used alone or in combination with each other for T2T genome assembly and characterization.

Proper citation: quarTeT (RRID:SCR_025258) Copy   

•   Source: SciCrunch Registry

https://github.com/xiaochuanle/NECAT

Software error correction and de-novo assembly tool for Nanopore long noisy reads. Nanopore data assembler.

Proper citation: NECAT (RRID:SCR_025350) Copy   

•   Source: SciCrunch Registry

https://github.com/PaulingLiu/ROGUE

Software tool as entropy-based metric for assessing purity of single cell populations. Used to accurately quantify purity of identified cell clusters.

Proper citation: ROGUE (RRID:SCR_026568) Copy   

•   Source: SciCrunch Registry

https://www.uii-ai.com/research.html

AI-powered integrated research platform for one-stop analysis of medical images. Provides advanced functionality such as automatic segmentation, registration, and classification for variety of application domains. Has major merits including Advanced built-in algorithms applicable to multiple imaging modalities (i.e., CT, MR, PET, DR), diseases (i.e., tumor, neurodegenerative disease, pneumonia), and applications (i.e., diagnosis, treatment planning, follow-up); Iterative deep learning-based training strategy for fast delineation of ROIs of large-scale datasets, thereby saving clinicians' time and obtaining novel and more robust models; Modular architecture with customization and extensibility, where plugins can be designed for specific purposes.

Proper citation: uAI Research Portal (RRID:SCR_025870) Copy   

•   Source: SciCrunch Registry

https://cadd.labshare.cn/cb-dock2/php/index.php

Web server for protein-ligand blind docking, integrating cavity detection, docking and homologous template fitting. Given the three-dimensional structure of protein and ligand, can predict their binding sites and affinity for computer-aided drug discovery.

Proper citation: CB-dock2 (RRID:SCR_026134) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/DOSE.html

Software R package for disease ontology semantic and enrichment analysis.

Proper citation: DOSE (RRID:SCR_027408) Copy   

•   Source: SciCrunch Registry

https://github.com/zhongguojie1998/CSOmap

Software tool for reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly. Infers cellular spatial organization from scRNA-seq by modeling ligand–receptor-mediated self-assembly. It constructs 3D pseudo-space and quantifies cell–cell interactions for downstream visualization and hypothesis testing.

Proper citation: CSOmap (RRID:SCR_027636) Copy   

•   Source: SciCrunch Registry

https://academic.oup.com/bioinformatics/article/34/7/1229/4657077

Software R/Shiny application for interactive creation of Circos plot. Used for creation of Circos plot interactively.

Proper citation: shinyCircoss (RRID:SCR_022367) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/rshrf

Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images.

Proper citation: Resting State Hemodynamic Response Function Retrieval and Deconvolution (RRID:SCR_023663) Copy   

•   Source: SciCrunch Registry