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https://bioconductor.org/packages/release/data/annotation/html/hgu133plus2.db.html

Software R package for Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data assembled using data from public repositories.

Proper citation: hgu133plus2 (RRID:SCR_026448) 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://github.com/NC4Lab/NC4gate

Code for testing and operating NC4gate modules of modular gate system for autonomous control of rodent behavior. Fully customizable gate system that can be used in behavioral experiments involving rodent mazes (T-maze, Y-maze, radial arm, etc.).

Proper citation: NC4gate (RRID:SCR_026445) 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://www.gnu.org/software/gettext/

Software tools that provide framework to help other GNU packages produce multi-lingual messages.

Proper citation: gettext (RRID:SCR_026490) 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/fzj-inm1-bda/siibra-python/

Software interface for interacting with brain atlases. Python client to brain atlas framework that integrates brain parcellations and reference spaces at different spatial scales, and connects them with broad range of multimodal regional data features. It aims to facilitate programmatic and reproducible incorporation of brain parcellations and brain region features from different sources into neuroscience workflows.

Proper citation: siibra-python (RRID:SCR_026596) 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/Knowledge-Graph-Hub/kg-microbe.git

Software tool as framework for knowledge graph construction and the current 4 KGs. Used to extract and integrate diverse knowledge about microbes from variety of structured and unstructured sources.

Proper citation: kg-microbe (RRID:SCR_026589) Copy   

•   Source: SciCrunch Registry

https://github.com/snowformatics/siFi21-?tab=readme-ov-file

Software tool for RNAi-target design and off-target prediction. Used for long double-stranded RNAi-target design and off-target prediction.

Proper citation: siFi (RRID:SCR_026556) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v79.html

Software ensembl based annotation R package. Exposes annotation databases generated from Ensembl. This package loads SQL connection to database containing annotations from Ensembl.

Proper citation: EnsDbHsapiensv79 (RRID:SCR_026703) 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/myvivarium/MyVivarium

Cloud-based lab animal colony management application with realtime ambient sensing. Platform for managing vivaria. It features cage management, user management, lab management, and real-time environmental monitoring with IoT sensors.

Proper citation: MyVivarium (RRID:SCR_026660) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/csaw/

Software R package for detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

Proper citation: CSAW (RRID:SCR_026738) Copy   

•   Source: SciCrunch Registry