Tools   Select Another Resource Report Type

https://autodocksuite.scripps.edu/adt/

Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure.

Proper citation: AutoDockTools (RRID:SCR_026401) Copy   

•   Source: SciCrunch Registry

https://github.com/spreka/biomagdsb

Software tool as parameter-free deep learning framework for nucleus segmentation using image style transfer. Cell segmentation tool.

Proper citation: NucleAIzer (RRID:SCR_026500) Copy   

•   Source: SciCrunch Registry

https://ecog-acrin.org/resources/ecog-performance-status/

ECOG Performance Scale describes patient’s level of functioning in terms of their ability to care for themself, daily activity, and physical ability (walking, working, etc.). Standard criteria for measuring how the disease impacts patient’s daily living abilities. Used to assess the functional status of patient.

Proper citation: Eastern Cooperative Oncology Group Performance Status Scale (RRID:SCR_026432) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=timeROC

Software R package for estimation of time-dependent ROC curve and area under time dependent ROC curve in the presence of censored data, with or without competing risks. Confidence intervals of AUCs and tests for comparing AUCs of two rival markers measured on the same subjects can be computed, using the iid-representation of the AUC estimator.

Proper citation: timeROC (RRID:SCR_026444) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=hdf5r

Software R package as data model, library and file format for storing and managing large amounts of data.

Proper citation: hdf5r (RRID:SCR_026447) Copy   

•   Source: SciCrunch Registry

https://github.com/agshumate/Liftoff

Software genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Aligns genes from reference genome to target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. Used for accurate mapping of gene annotations.

Proper citation: Liftoff (RRID:SCR_026535) Copy   

•   Source: SciCrunch Registry

https://igit.informatik.htw-dresden.de/aagef650/spheroidsegdedeb

Software minimal tool for segmentation of irradiated tumor spheroids using optimized U-Net.

Proper citation: SpheroidSegDeDeb (RRID:SCR_026409) Copy   

•   Source: SciCrunch Registry

https://github.com/ddarriba/modeltest

Software tool for selecting the best-fit model of evolution for DNA and protein alignments. Used for selection of DNA and Protein evolutionary models.

Proper citation: modeltest (RRID:SCR_026633) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/ssGSEA2.0

Software application as updated version of original ssGSEA R-implementation. Depending on the input dataset and chosen database (gene sets or PTM signatures), the software performs either ssGSEA or PTM-SEA, respectively.

Proper citation: ssGSEA 2.0 (RRID:SCR_026610) Copy   

•   Source: SciCrunch Registry

https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2

Software tool to call somatic short mutations via local assembly of haplotypes. Somatic variant caller that uses local assembly and realignment to detect SNVs and indels.

Proper citation: Mutect2 (RRID:SCR_026692) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/statannotations/

Software Python package to optionally compute statistical test and add statistical annotations on plots generated with seaborn. Used to add statistical significance or custom annotations on seaborn plots.

Proper citation: statannotations (RRID:SCR_026623) Copy   

•   Source: SciCrunch Registry

https://github.com/Breeding-Insight/BIGapp

Species-agnostic web-based application for processing genotypic data in no-code RShiny user-friendly interface. Allows users without coding experience to process genetic data in all genome ploidy ranges and for multiallelic data, starting from number of input formats (including VCF). Also allows to perform downstream QC analyses (e.g., PCA) and run genomic analysis (e.g., Linkage mapping, QTL analysis, genome-wide association studies (GWAS), and genomic selection (GS).

Proper citation: BIGapp (RRID:SCR_026676) Copy   

•   Source: SciCrunch Registry

https://github.com/Breeding-Insight/bi-web

Breeding-Insight/bi-web development.

Proper citation: bi-web (RRID:SCR_026678) Copy   

•   Source: SciCrunch Registry

https://github.com/SchapiroLabor/phenoimager2mc

Software tool for formatting PhenoImager TIFF/OME-TIFF metadata for compatibility with MCMICRO workflow.

Proper citation: phenoimager2mc (RRID:SCR_026561) Copy   

•   Source: SciCrunch Registry

https://github.com/higlass/higlass

Web-based visual exploration and analysis of genome interaction maps.

Proper citation: HiGlass (RRID:SCR_026687) Copy   

•   Source: SciCrunch Registry

https://github.com/tabatsky/projectionpursuit

Software tool for automated projection pursuit clustering. Alternative clustering approach that alleviates the curse of dimensionality by sequentially projecting high-dimensional data into a low-dimensional representation.

Proper citation: Automated Projection Pursuit (RRID:SCR_026560) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/rrvgo/

Software R package to reduce and visualize Gene Ontology terms. Used for interpreting lists of Gene Ontology terms.

Proper citation: rrvgo (RRID:SCR_026680) Copy   

•   Source: SciCrunch Registry

https://github.com/sridevi96/NeuroDevTime

Software code for age prediction in fetal brain and organoid single cell data. This repository contains cell type agnostic models to predict the developmental age of brain cell types from single cell RNAseq data. Code contains 4 jupyter notebooks, which apply pretrained models to predict neurodevelopmental age of cell types in new human fetal brain and organoid datasets.

Proper citation: NeuroDevTime (RRID:SCR_026651) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/WebWarp

Web application for nonlinear refinement of image registration after WebAlign.

Proper citation: WebWarp (RRID:SCR_026759) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/WebAlign

Web application for 2D image registration to 3D atlas. Used for user guided affine spatial registration (anchoring) of sectional image data, typically high resolution histological images, to 3D reference atlas space. Can generate user defined cut planes through atlas templates that match orientation of cutting plane of 2D experimental images (atlas maps).

Proper citation: WebAlign (RRID:SCR_026758) Copy   

•   Source: SciCrunch Registry