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https://bioconductor.org/packages/release/bioc/html/BayesSpace.html

Software R package for clustering and enhancing resolution of spatial gene expression experiments. Clusters low-dimensional representation of gene expression matrix, incorporating spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

Proper citation: BayesSpace (RRID:SCR_026309) Copy   

•   Source: SciCrunch Registry

http://qualimap.conesalab.org/

Software platform-independent application written in Java and R that provides both Graphical User Inteface and command-line interface to facilitate quality control of alignment sequencing data and its derivatives like feature counts. Used for advanced multi-sample quality control for high-throughput sequencing data.

Proper citation: Qualimap 2 (RRID:SCR_026258) Copy   

•   Source: SciCrunch Registry

https://github.com/mwess/greedyfhist

Algorithm for registration of stained fresh frozen serial images. Used for registration of stained histology images.

Proper citation: GreedyFHist (RRID:SCR_026477) Copy   

•   Source: SciCrunch Registry

https://github.com/wilkelab/ggtext/

Software R package that enhances text rendering in ggplot2 by allowing the use of Markdown, HTML, and rich text formatting for annotations, labels, and titles in plots.

Proper citation: ggtext (RRID:SCR_026470) Copy   

•   Source: SciCrunch Registry

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

Software R package as dissimilarity-based functions for ecological analysis. Used for analyzing ecological data.

Proper citation: ecodist (RRID:SCR_026509) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/chopper

Software tool that combines the utility of NanoFilt and NanoLyse, for filtering sequencing reads based on quality, length, and contaminating sequences, delivers 7-fold speed up compared to the Python implementation, making use of the Rust-Bio library and Rust bindings to minimap2.

Proper citation: chopper (RRID:SCR_026486) Copy   

•   Source: SciCrunch Registry

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