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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

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

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://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://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://bio-comp.org.cn/llpsdb/home.html

Database of proteins undergoing liquid–liquid phase separation in vitro. Contains LLPS related proteins together with the corresponding phase separation conditions validated by experiments.

Proper citation: LLPSDB (RRID:SCR_024966) 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.rnaphasep.cn/#/Home

Database that collects phase separation related RNAs manually curated from publication and public databases.

Proper citation: RNAPhaSep (RRID:SCR_024958) 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

http://spatialomics.org/SpatialDB/

Database for spatially resolved transcriptomes. Provides curated spatially resolved transcriptomic data from published papers, aiming to provide comprehensive and accurate resource of spatial gene expression profiles in tissues. Allows users to browse spatial gene expression profile and compare spatial gene expression profile of any two datasets generated by same or different techniques side by side.

Proper citation: Spatial DB (RRID:SCR_026135) 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

http://herb.ac.cn/

High-throughput experiment- and reference-guided database of traditional Chinese medicine.

Proper citation: HERB (RRID:SCR_026468) 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

http://www.zhounan.org/ferrdb/current/

Manually curated database of ferroptosis regulators and ferroptosis-disease associations. There are two secondary categories of ferroptosis regulators: (1) genes and (2) substances. Gene regulators include driver, suppressor, marker, and unclassified regulator. Substances cover range of chemical entities, including pure substances (e.g., iron, erastin) and mixtures (e.g., herbal extracts). Substance regulators include inducers and inhibitors. FerrDb V2 is updated database.

Proper citation: FerrDb (RRID:SCR_026852) 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

http://ctrdb.ncpsb.org.cn/

Data resource for clinical transcriptomes with cancer treatment response, and meanwhile supports various data analysis functions, providing insights into the molecular determinants of drug resistance. CTR-DB 2.0 is updated cancer clinical transcriptome resource, expanding primary drug resistance and newly adding acquired resistance datasets and enhancing the discovery and validation of predictive biomarkers.

Proper citation: Cancer Treatment Response gene signature DataBase (RRID:SCR_027950) Copy   

•   Source: SciCrunch Registry