Tools   Select Another Resource Report Type

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

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

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://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/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://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://idm.fudan.edu.cn/PBmice/

Database for storing, retrieving, and displaying the information derived from piggyBac (PB) insertions (Insert) and their characterizations in the mouse genome with piggyBac transposon system. Quick Search and Advanced Search tools have been provided to find information in the PBmice database, the result is centered on Inserts and provides information related to the Inserts. A mapping database is linked to PBmice too. This mapping database allows row experiment data to be inputted in. All the mature data can be allowed publish to PBmice. PBmice Source Code is available with a License Agreement.

Proper citation: PBmice (RRID:SCR_006978) 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://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://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

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

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

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/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