Tools   Select Another Resource Report Type

https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2

Software integrative pipeline for antimicrobial resistance genes, virulence factors, toxins, and biosynthetic gene clusters prediction in metagenomes. Used for predicting microbiome-based pathogenicity and resistance to better understand and address challenges posed by antimicrobial resistance and infectious diseases.

Proper citation: PathoFact2 (RRID:SCR_027650) Copy   

•   Source: SciCrunch Registry

https://www.github.com/bactopia/bactopia

Software pipeline for complete analysis of bacterial genomes.

Proper citation: Bactopia (RRID:SCR_027581) Copy   

•   Source: SciCrunch Registry

https://github.com/INCF/swc-specification

Software repository contains files needed to build the standard and its supplementary documentation. Changes are automatically pushed and built. Information about the SWC file specification.

Proper citation: SWC format (RRID:SCR_027631) Copy   

•   Source: SciCrunch Registry

https://novosparc.readthedocs.io/

Software package for flexible spatial reconstruction of single-cell gene expression with optimal transport. Framework for de novo spatial reconstruction of single-cell gene expression. Assigns cells to tissue locations using probabilistic/optimal-transport models, with or without prior marker information, and returns spatial maps and assignment probabilities.

Proper citation: novoSpaRc (RRID:SCR_027635) Copy   

•   Source: SciCrunch Registry

https://alleninstitute.github.io/CCF-MAP/docs/HOMBA_ontology_v1.html

Harmonized cross-species taxonomy of brain and spinal cord structures. Derived from the Allen Developing Human Brain Atlas (DHBA) ontology, the HOMBA is hierarchical, allowing users to aggregate structures from fine grain parcellations to broad regions. Terminology is harmonized across human, primate, and rodent structures with synonymous terms and includes transient developmental structures. HOMBA is designed for neuroanatomical applications including brain sampling and dissection, tissue block mapping, atlas building, cell-type and pathology localization, and linking cross-species and developmental datasets.

Proper citation: Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) (RRID:SCR_027628) Copy   

•   Source: SciCrunch Registry

https://stardist.net/

Software application for object detection with Star-convex Shapes. Used for phase-contrast cell images.

Proper citation: StarDist (RRID:SCR_027715) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/bbglab/oncodriveclustl/src/master

Software application to detect significant clustering signals across genomic regions. Sequence-based clustering method to identify cancer drivers.

Proper citation: OncodriveCLUSTL (RRID:SCR_027730) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/bbglab/oncodrivefml/src/master

Software tool that estimates accumulated functional impact bias of somatic mutations in any genomic region of interest based on local simulation of the mutational process affecting it.

Proper citation: OncodriveFML (RRID:SCR_027731) Copy   

•   Source: SciCrunch Registry

https://github.com/instadeepai/instanovo

Source code for training and inference of InstaNovo and InstaNovo+. InstaNovo is a transformer neural network with the ability to translate fragment ion peaks into the sequence of amino acids that make up the studied peptide(s).

Proper citation: InstaNovo (RRID:SCR_027758) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=AER

Software R package contains functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.

Proper citation: AER: Applied Econometrics with R (RRID:SCR_027778) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ActivePathways/index.html

Software R package for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets.Method that first prioritises genes through multi-omics data fusion and then identifies enriched pathways with gene-level evidence from input datasets.

Proper citation: ActivePathways (RRID:SCR_027736) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html

Software R package containing the full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31).

Proper citation: BSgenome Hsapiens UCSC hg38 (RRID:SCR_027738) Copy   

•   Source: SciCrunch Registry

https://github.com/zhoujt1994/scHiCluster

Software Python package for single-cell chromosome contact data analysis. It includes the identification of cell types (clusters), loop calling in cell types, and domain and compartment calling in single cells. Facilitates visualization and comparison of single-cell 3D genomes.

Proper citation: scHiCluster (RRID:SCR_027854) Copy   

•   Source: SciCrunch Registry

https://opensourcephysics.github.io/tracker-website/

Software video analysis and modeling tool developed within the Open Source Physics (OSP) Java framework. Allows frame-by-frame tracking of anatomical landmarks and articulated structures from video recordings, enabling the extraction of time-dependent kinematic variables such as displacement, velocity, and acceleration. Tracker is well suited for biomechanical analyses of articulated systems, as it supports joint-based rotations, reference-frame definition, and the export of quantitative motion data for further post-processing.

Proper citation: Tracker (RRID:SCR_027845) Copy   

•   Source: SciCrunch Registry

https://github.com/mzlab-research/SMIntegration

Software open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Enables to explore gene-metabolite co-regulation mechanisms through an intuitive web interface, revealing spatial heterogeneity in tissue development and disease progression.

Proper citation: SMIntegration (RRID:SCR_027925) Copy   

•   Source: SciCrunch Registry

https://github.com/NOW-Lab/STICR

Code to conduct combinatorial barcoding. scRNA-seq-compatible tracer for identifying clonal relationships.

Proper citation: STICR (RRID:SCR_027856) Copy   

•   Source: SciCrunch Registry

https://github.com/blaserlab/blaseRtools/tree/v0.0.0.9202

Software R tools for Blaser Lab Data Analysis. Package includes commonly used functions for R analysis in the Blaser Lab.

Proper citation: blaseRtools (RRID:SCR_027871) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/sivic/

Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.

Proper citation: Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) Copy   

•   Source: SciCrunch Registry

https://bio.tools/dupradar

Software R package for assessment of PCR artifacts in RNA-Seq data. Used for duplication rate quality control for RNA-Seq datasets.

Proper citation: dupRadar (RRID:SCR_027976) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexanRNA/nanowgs/releases/tag/v0.0.2

Nextflow pipeline to process whole genome long-read sequencing data generated in the context of ASAP project.

Proper citation: NanoWGS (RRID:SCR_028113) Copy   

•   Source: SciCrunch Registry