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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://cran.r-project.org/web/packages/BAMMtools/index.html
Software R package for analysis and visualization of macroevolutionary dynamics on phylogenetic trees.
Proper citation: BAMMtools (RRID:SCR_027137) Copy
https://github.com/hartwigmedical/hmftools/tree/master/cobalt
Software tool to determine read depth ratios of supplied tumor and reference genomes.
Proper citation: COBALT (RRID:SCR_027132) Copy
Video analysis software designed for the study of animal behavior.
Proper citation: Ethotrack (RRID:SCR_027105) Copy
https://github.com/gillislab/MetaMarkers
Software R package to efficiently compute robust markers across single-cell datasets. Robust marker signatures from single-cell data.
Proper citation: MetaMarkers (RRID:SCR_027104) Copy
https://cran.r-project.org/web/packages/babelgene/index.html
Software R package to convert between human and non-human gene orthologs/homologs. Integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 , Eyre et al. 2007 , Seal et al. 2011 ).
Proper citation: babelgene (RRID:SCR_027117) Copy
https://bioconductor.org/packages/release/bioc/html/UCell.html
Software package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects.
Proper citation: UCell (RRID:SCR_027109) Copy
https://cran.r-project.org/web/packages/flexmix/index.html
Software R package for finite mixtures of regression models using EM algorithm. General framework for finite mixture models and latent class regression in R.
Proper citation: flexmix (RRID:SCR_027152) Copy
https://github.com/DianeDuroux/ZeroShotAMR
Software repository provides the code for generalizable machine learning models for rapid antimicrobial resistance prediction in unseen healthcare settings.
Proper citation: ZeroShotAMR (RRID:SCR_027224) Copy
https://github.com/aametwally/Metabolic_Subphenotype_Predictor
Software repository contains code for Inference of T2D metabolic subphenotypes (MuscleIR, Beta-cell Function, Incretin Effect, Hepatic IR), Identification of dominant metabolic subphenotype, Feature extraction from glucose tiemseries, Extraction of reduced representation of glucose tiemseries,Visualization of metabolic phenotypes based on various glucose-related metrics,Concordance between CGM and Venous glucose values from at home and at clinical setting, Classification of metabolic subphenotypes.
Proper citation: Metabolic Subphenotype Predictor (RRID:SCR_027192) Copy
https://gitee.com/zhixingfeng/NanoFreeLunch.jl
Software toolkit for quantitative detection of DNA methylation from nanopore sequencing data without raw signals.
Proper citation: NanoFreeLunch (RRID:SCR_027196) Copy
https://www.bioconductor.org/packages/release/bioc/html/IsoformSwitchAnalyzeR.html
Software R package to identify, annotate and visualize isoform switches with functional consequences from both short- and long-read RNA-seq data. Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.
Proper citation: IsoformSwitchAnalyzeR (RRID:SCR_027320) Copy
https://github.com/ngyuilun/EC-LMGraph
Software tool, which combine graph deep learning and protein language model, for accurate enzyme function and catalytic site prediction.
Proper citation: EC-LMGraph (RRID:SCR_027317) Copy
https://github.com/janjoy/BTE-RAG
Software application for BTE RAG implementation for DMDB QA datasets. Provides implementation of BTE-RAG framework, designed specifically for retrieval-augmented question answering (QA) in biomedical contexts. BTE-RAG leverages explicit mechanistic knowledge retrieval from BioThings Explorer (BTE) to significantly enhance the accuracy and reliability of large language models (LLMs) on biomedical benchmarks.
Proper citation: BTE-RAG (RRID:SCR_027297) Copy
https://www.bioconductor.org/packages/release/bioc/html/sesame.html
Software R package for reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.
Proper citation: SeSAMe (RRID:SCR_027388) Copy
https://rfxplot.sourceforge.net/
Software toolbox for SPM5 which offers plotting effect sizes, fitted responses, and BOLD time courses averaged across subjects from within 2nd level (random effects) analyses. The toolbox offers a large variety of plot configuration both suitable for data exploration and producing high quality figures for publications.
Proper citation: rfxplot (RRID:SCR_027375) Copy
https://cloud.sylabs.io/library/jsaraiva/repo/hvrlocator
Software application to identify spanning hypervariable region(s) from amplicon sequencing variants or SRA public runs (SRR). Aligns query sequences to reference E. coli full-length 16S rRNA gene and identifies spanning region through alignment. Used for identifying hypervariable regions in 16S rRNA big datasets.
Proper citation: HVRLocator (RRID:SCR_027407) Copy
https://github.com/rnajena/dynamont
Software segmentation/resquiggling tool for ONT signals. Dynamic programming approach to segment ONT signals.
Proper citation: Dynamont (RRID:SCR_027357) Copy
https://brain-bican.github.io/bkbit/
Software package contains tools to use the BICAN Knowledgebase Data Models.
Proper citation: bkbit (RRID:SCR_027564) Copy
Open-source software Python library that provides high-level interface for PyTorch deep learning framework.
Proper citation: PyTorch Lightning (RRID:SCR_027468) Copy
https://github.com/aertslab/create_cisTarget_databases
Code to create cisTarget databases.
Proper citation: create_cisTarget_databases (RRID:SCR_027473) Copy
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