Tools   Select Another Resource Report Type

https://github.com/caaswxb/SRY

Software application for sorting long-read of sex-limited (Y or W) chromosome. Used to identify male specific k-mers based on population data.

Proper citation: Sorting long Reads of Y or other sex-limited chromosome (RRID:SCR_025036) Copy   

•   Source: SciCrunch Registry

https://ssbd.riken.jp/azebex/

Collection of in situ hybridization data of gene expression in the brain of adult fish. Data can be viewed and downloaded.

Proper citation: Adult Zebrafish Brain Gene Expression Database (RRID:SCR_025122) Copy   

•   Source: SciCrunch Registry

https://mutalyzer.nl/

Software suite is designed to be of help when working with Human Genome Variation Society sequence variant nomenclature descriptions.

Proper citation: LUMC Mutalyzer 3 (RRID:SCR_026148) Copy   

•   Source: SciCrunch Registry

http://tide.dfci.harvard.edu/login/

Web platform for large-scale public data reuse to model immunotherapy response and resistance. Provides integrated large-scale omics data and biomarkers on published ICB trials, non-immunotherapy tumor profiles, and CRISPR screens.

Proper citation: TIDE (RRID:SCR_026350) Copy   

•   Source: SciCrunch Registry

https://github.com/labcbb/SqueezeCall

Software tool as Nanopore basecalling using Squeezeformer network to improve basecalling accuracy over recurrent neural network (RNN)-based model and Transformer-based models.

Proper citation: SqueezeCall (RRID:SCR_026321) Copy   

•   Source: SciCrunch Registry

https://github.com/SoSongzhi/PVGA

Software tool as virus-focused assembler that does both assembly and polishing into unified workflow. Viral genome assembler enables detection of subtle genomic variations that can significantly impact viral function and pathogenicity.

Proper citation: PVGA (RRID:SCR_026410) Copy   

•   Source: SciCrunch Registry

https://github.com/JLSteenwyk/ClipKIT

Software fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others. Multiple sequence alignment-trimming algorithm for accurate phylogenomic inference.

Proper citation: ClipKIT (RRID:SCR_026411) Copy   

•   Source: SciCrunch Registry

https://github.com/ZhantianXu/PISAD

Software reference-free intraspecies sample anomalies detetion tool based on k-mer counting.

Proper citation: PISAD (RRID:SCR_026597) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/CreateZoom/tree/main

Backend application to process high-resolution histology images to DeepZoomImage format, made of smaller tiles, for use in the QUINT Workflow.

Proper citation: CreateZoom (RRID:SCR_026625) Copy   

•   Source: SciCrunch Registry

https://www.polebio.lrsv.ups-tlse.fr/WallProtDB/

Database resource for plant cell wall proteomics. Aims at collecting cell wall proteomic experimental data. For each experiment, a scheme summarizing the strategy used for protein isolation and identification is provided.

Proper citation: WallProtDB (RRID:SCR_026506) Copy   

•   Source: SciCrunch Registry

https://ruggleslab.shinyapps.io/RIVET/

Software tool to automate statistical analysis of RNA seq data acquired from polysome profile or ribosome footprinting experiments.

Proper citation: RIVET (RRID:SCR_026488) Copy   

•   Source: SciCrunch Registry

https://archive.ics.uci.edu/

Collection of databases, domain theories, and data generators that are used by machine learning community for empirical analysis of machine learning algorithms. Datasets approved to be in the repository will be assigned Digital Object Identifier (DOI) if they do not already possess one. Datasets will be licensed under a Creative Commons Attribution 4.0 International license (CC BY 4.0) which allows for the sharing and adaptation of the datasets for any purpose, provided that the appropriate credit is given

Proper citation: UCI Machine Learning Repository (RRID:SCR_026571) Copy   

•   Source: SciCrunch Registry

https://github.com/melobio/Attune

Software framework for integrating gene expression and chromatin accessibility, enabling the inference of regulatory mechanisms and the prediction of gene expression from cross-modal data. Repository contains code and tutorials for the following tasks: multimodal pretraining, cross-modal prediction, inferring regulatory network and potential analysis.

Proper citation: Attune (RRID:SCR_026494) Copy   

•   Source: SciCrunch Registry

https://endomap.hms.harvard.edu/

Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes.

Proper citation: EndoMap (RRID:SCR_026690) Copy   

•   Source: SciCrunch Registry

https://github.com/YuningHao/FARDEEP

Software R tool for enumerating immune cell subsets from whole tumor tissue samples. Utilizes adaptive least trimmed square to automatically detect and remove outliers before estimating cell compositions.

Proper citation: FARDEEP (RRID:SCR_026704) Copy   

•   Source: SciCrunch Registry

https://markerdb.ca/

Database that attempts to consolidate information on known clinical and selected set of pre-clinical biomarkers into single resource. Database includes five major types of biomarkers (condition specific, protein, chemical, karyotypic and genetic) and six biomarker categories (diagnostic, risk, prognostic, safety, monitoring, and response). Provides information such as: biomarker names and synonyms, associated conditions or pathologies, detailed disease descriptions, detailed biomarker descriptions, biomarker specificity, sensitivity and ROC curves, standard reference values (for protein and chemical markers), variants (for SNP or genetic markers), sequence information (for genetic and protein markers), molecular 2D and 3D structures (for protein and chemical markers), tissue or biofluid sources (for protein and chemical markers), chromosomal location and structure (for genetic and karyotype markers), clinical approval status and relevant literature references. Users can browse the data by conditions, condition categories, biomarker types, biomarker categories or search by sequence similarity through the advanced search function.

Proper citation: MarkerDB (RRID:SCR_026817) Copy   

•   Source: SciCrunch Registry

https://microbiomap.org

Microbial ecology dataset describing the composition of publicly available human microbiome samples deposited in INSDC databases (Sequence Read Archive, European Nucleotide Archive, Digital Data Bank of Japan). Genus-level read counts are available for more than 168,000 samples from around the world, with additional curated metadata for samples and projects.

Proper citation: Human Microbiome Compendium (RRID:SCR_026991) Copy   

•   Source: SciCrunch Registry

https://gdex.ucar.edu/

Provides data for atmospheric and ocean sciences research. Contains collection of meteorological, atmospheric composition, and oceanographic observations, and operational and reanalysis model outputs, integrated with NSF NCAR High Performance Compute services to support atmospheric and geosciences research. The RDA is managed by the Data Engineering and Curation Services group of the Computational and Information Systems Laboratory at the NSF National Center for Atmospheric Research.

Proper citation: The Geoscience Data Exchange (RRID:SCR_026989) Copy   

•   Source: SciCrunch Registry

https://tp53.cancer.gov/

Database compiles various types of data and information from literature and generalist databases on human TP53 gene variations related to cancer.

Proper citation: TP53 Database (RRID:SCR_026878) Copy   

•   Source: SciCrunch Registry

https://github.com/inesbmartins02/HYMET

Software Hybrid Metagenomic Tool.

Proper citation: HYMET (RRID:SCR_026916) Copy   

•   Source: SciCrunch Registry