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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

http://wego.genomics.org.cn/cgi-bin/wego/index.pl

Web Gene Ontology Annotation Plot (WEGO) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. Platform: Online tool

Proper citation: WEGO - Web Gene Ontology Annotation Plot (RRID:SCR_005827) Copy   

•   Source: SciCrunch Registry

http://huanglab.phys.hust.edu.cn/hpepdock/

Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations.

Proper citation: HPEPDOCK Server (RRID:SCR_018561) Copy   

•   Source: SciCrunch Registry

http://easybioai.com/sc2disease/

Manually curated database of single cell transcriptome for human diseases. scRNA-seq database derived from numerous human studies. Provides researchers with encyclopedia of biomarkers at level of genes, cells, and diseases.

Proper citation: SC2diseases (RRID:SCR_019093) Copy   

•   Source: SciCrunch Registry

https://github.com/YangLab/CLEAR

Software tool as computational pipeline for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq. CIRCexplorer3-CLEAR is CLEAR pipeline for direct comparison of circular and linear RNA expression.

Proper citation: CLEAR (RRID:SCR_021663) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/gig-ica/

Software toolbox for group-information guided Independent Component Analysis (ICA). In GIG-ICA, group information captured by standard Independent Component Analysis (ICA) on the group level is used as guidance to compute individual subject specific Independent Components (ICs) using a multi-objective optimization strategy. For computing subject specific ICs, GIG-ICA is applicable to subjects that are involved or not involved in the computation of the group information. Besides the group ICs, group information captured from other imaging modalities and meta analysis could be used as the guidance in GIG-ICA too.

Proper citation: Group Information Guided ICA (RRID:SCR_009491) 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

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://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://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://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