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https://tcmsp-e.com/tcmsp.php

Pharmacology platform of Chinese herbal medicines that captures relationships between drugs, targets and diseases. Database includes chemicals, targets and drug-target networks, and associated drug-target-disease networks, as well as pharmacokinetic properties for natural compounds involving oral bioavailability, drug-likeness, intestinal epithelial permeability, blood-brain-barrier, aqueous solubility.

Proper citation: Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (RRID:SCR_023757) Copy   

•   Source: SciCrunch Registry

http://isyslab.info/NeuroPep/

Comprehensive resource of neuropeptides, which holds non-redundant neuropeptide entries. Data collected from resources including MEDLINE abstracts, full papers, UniProt,database at www.neuropeptides.nl and Neuropedia. Contains detailed annotations for each entry, including source organisms, tissue specificity, families, names, post-translational modifications, 3D structures and literature references. Amino acid compositions, isoelectric points, molecular weight and other physicochemical properties of peptides are also provided. Search database with keywords such as sequence, name, family, etc.,User friendly web tools like browsing, sequence alignment and mapping are also integrated.Users can submit new entries online. Each new entry is validated before incorporating it.

Proper citation: NeuroPep (RRID:SCR_023102) Copy   

•   Source: SciCrunch Registry

https://open.oncobox.com/

Structured curated collection of protein based and of metabolic human molecular pathways. Human molecular pathways database with tools for activity calculating and visualization.All pathways are functionally classified according to GO terms enrichment patterns. All pathway participants, their interactions and reactions are uniformly processed and annotated, and are ready for numeric analysis of experimental expression data.For every comparison graph is generated summarizing top up and down regulated pathways.

Proper citation: OncoboxPD (RRID:SCR_023723) Copy   

•   Source: SciCrunch Registry

http://brassicadb.cn

Database includes newly released genome sequences of Brassiceae species and published genomic data of most other Brassicaceae species.Data can be browsed in JBrowse or searched in BLAST. Offers service of searching for syntenic genes, which are generated based on their syntenic relationships to genes in Arabidopsis thaliana. Regularly updated with newly released reference genomes.

Proper citation: Brassicaceae Database (RRID:SCR_023019) Copy   

•   Source: SciCrunch Registry

http://bis.zju.edu.cn/DaTo/

A biological database and software tool catalog based on text mined and human annotated url mentions in PubMed abstracts. Data are annotated as to the author''''s country of origin and url status is checked.

Proper citation: DaTo (RRID:SCR_010280) Copy   

•   Source: SciCrunch Registry

https://orthovenn2.bioinfotoolkits.net/home

Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences.

Proper citation: OrthoVenn2 (RRID:SCR_022504) Copy   

•   Source: SciCrunch Registry

http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/

Web application for predicting subcellular localization of plant proteins including those with multiple sites.Top Down Strategy to Augment Power for Predicting Plant Protein Subcellular Localization.

Proper citation: Plant mPLoc (RRID:SCR_023014) Copy   

•   Source: SciCrunch Registry

https://awi.cuhk.edu.cn/KinasePhos/download.html

Software tool for redesign and expansion of prediction on kinase specific phosphorylation sites. Machine learning based kinase specific phosphorylation site prediction tool.

Proper citation: KinasePhos 3.0 (RRID:SCR_023595) Copy   

•   Source: SciCrunch Registry

https://ngdc.cncb.ac.cn/databasecommons/

Curated catalog of worldwide biological databases to provide landscape of biological databases throughout the world and enable easy retrieval and access to specific collection of databases of interest. Catalog of worldwide biological databases as well as their curated meta information and derived statistics.

Proper citation: Database Commons (RRID:SCR_023661) Copy   

•   Source: SciCrunch Registry

http://bioinfo.jialab-ucr.org/CancerMIRNome/

Web server for cancer miRNome interactive analysis and visualization based on human miRNome data of cancer types from The Cancer Genome Atlas, and public cancer circulating miRNome profiling datasets from NCBI Gene Expression Omnibus and ArrayExpress. Comprehensive database for interactive analysis and visualization of miRNA expression profiles.

Proper citation: CancerMIRNome (RRID:SCR_022092) Copy   

•   Source: SciCrunch Registry

https://funricegenes.github.io/

Dataset of functionally characterized rice genes and members of different gene families. The dataset was created by integrating data from available databases and reviewing publications of rice functional genomic studies.

Proper citation: funRiceGenes (RRID:SCR_015778) Copy   

•   Source: SciCrunch Registry

https://github.com/esctrionsit/snphub

Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data.

Proper citation: SnpHub (RRID:SCR_018177) Copy   

•   Source: SciCrunch Registry

http://gepia.cancer-pku.cn

Web server for cancer and normal gene expression profiling and interactive analyses. Interactive web server for analyzing RNA sequencing expression data of tumors and normal samples from TCGA and GTEx projects, using standard processing pipeline. Provides customizable functions such as tumor or normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis.

Proper citation: Gene Expression Profiling Interactive Analysis (RRID:SCR_018294) Copy   

•   Source: SciCrunch Registry

http://sumosp.biocuckoo.org.

Web service for prediction of SUMOylation sites and SUMO-interaction motifs in proteins by CUCKOO Workgroup.

Proper citation: GPS-SUMO (RRID:SCR_018261) Copy   

•   Source: SciCrunch Registry

https://cistrome.shinyapps.io/timer/

Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features.

Proper citation: TIMER (RRID:SCR_018737) Copy   

•   Source: SciCrunch Registry

https://cgmaptools.github.io

Software package for DNA methylation analysis. Used for context-wise, gene-wise, bin-wise, region-wise and sample-wise analysis and visualizations. Used to improve precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.

Proper citation: cgmapotools (RRID:SCR_020950) Copy   

•   Source: SciCrunch Registry

https://yanglab.nankai.edu.cn/trRosetta/

Software tool for fast and accurate protein structure prediction. Builds protein structure based on direct energy minimizations with restrained Rosetta. Restraints include inter-residue distance and orientation distributions, predicted by deep residual neural network. Homologous templates are included in network prediction to improve accuracy for easy targets.

Proper citation: trRosetta (RRID:SCR_021181) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-biols/CIRIquant

Software Python package for accurate circRNA quantification and differential expression analysis. Comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data. Accurate quantification of circular RNAs identifies extensive circular isoform switching events.

Proper citation: CIRIquant (RRID:SCR_021661) Copy   

•   Source: SciCrunch Registry

https://circexplorer2.readthedocs.io/en/latest/

Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs.

Proper citation: CIRCexplorer2 (RRID:SCR_021664) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html

Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

Proper citation: clusterProfiler (RRID:SCR_016884) Copy   

•   Source: SciCrunch Registry