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https://github.com/cytoscape/RCy3

Software R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort.Network biology using Cytoscape from within R.

Proper citation: RCy3 (RRID:SCR_027668) Copy   

•   Source: SciCrunch Registry

https://www.augusta.edu/research/core/proteomics.php

Facility for characterization and expression level quantitation of proteins (isolated or in an extract) and small molecules/metabolites by mass spectrometry (MS) and/or chromatography. Services include protein identification, labeled and label-free comparative proteomics by Orbitrap mass spectometry, protein/small molecule quantification using targeted mass spectometry (PRM and SRM/MRM mass spectometry), high throughput protein immune-protein assays (384-well Luminex/ELISA assay), etc.

Proper citation: Augusta University Proteomics and Mass Spectrometry Core Facility (RRID:SCR_027673) Copy   

•   Source: SciCrunch Registry

https://www.solarbio.com/

Commercial vendor and service provider of laboratory reagents and antibodies located in Beijing, China. Supplier of scientific instrumentation, reagents and consumables, and software services.

Proper citation: Solarbio (RRID:SCR_027671) Copy   

•   Source: SciCrunch Registry

https://guolab.wchscu.cn/ImmuCellAI/#!/

Software tool for comprehensive T‐Cell subsets abundance prediction and its application in cancer immunotherapy.

Proper citation: ImmuCellAI (RRID:SCR_027645) Copy   

•   Source: SciCrunch Registry

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://atlantis.bioinfolab.sns.it

Integrative database for human proteome structural and functional sites. Used for understanding role of specific residues in protein structures, complexes, and interaction networks. Integrates various structural and functional annotation layers for each residue, offering comprehensive understanding of protein functionality.

Proper citation: Atlantis (RRID:SCR_027648) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/multiVIB

Software tool as comprehensive framework for integration of single-cell omics data with probabilistic contrastive learning.

Proper citation: multiVIB (RRID:SCR_027589) Copy   

•   Source: SciCrunch Registry

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

Software R package as Tidy API for graph manipulation. Graph can be thought of as two tidy data frames describing node and edge data respectively. Used to manipulate these two virtual data frames using API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.

Proper citation: tidygraph (RRID:SCR_027617) 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://github.com/AllenInstitute/AllenInstituteTaxonomy/tree/main/schema

Compartmentalized schema for storing all required aspects of taxonomy. Fields in AIT schema are associated to broad category term which form piece of whole AIT file format.

Proper citation: Allen Institute Taxonomy Standard (RRID:SCR_027629) Copy   

•   Source: SciCrunch Registry

https://bioserv.rpbs.univ-paris-diderot.fr/services/SeamDock/

Web server for interactive and collaborative online docking to assist small compound molecular docking. In silico assessment of protein receptor interactions with small ligands.

Proper citation: SeamDock (RRID:SCR_027686) Copy   

•   Source: SciCrunch Registry

https://github.com/keyuan/ccube

Software R package for clustering and estimating cancer cell fractions (CCF) of somatic variants (SNVs/SVs) from bulk whole genome/exome data. Used for estimating cancer cell fractions .

Proper citation: Ccube (RRID:SCR_027721) Copy   

•   Source: SciCrunch Registry

https://github.com/Wedge-lab/dpclust

Software R package containing methods for sub-clonal reconstruction through SNVs and/or CNAs from whole genome or whole exome sequencing data.

Proper citation: DPClust (RRID:SCR_027723) Copy   

•   Source: SciCrunch Registry

https://github.com/cancerit/ClusterSV

Software application to group genetic structural variant rearrangements into rearrangement clusters and footprints. Used in the PCAWG-6 project.

Proper citation: ClusterSV (RRID:SCR_027722) 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://fivepseq-explorer.serve.scilifelab.se/app/fivepseq-explorer

Web-based platform for interactive exploration of ribosome dynamics derived from 5′P mRNA degradome sequencing (5PSeq) data. Focused on changes in ribosome dynamics associated to mRNA decay that in some cases can be obscured in conventional ribosome profiling data.

Proper citation: 5PSeq Explorer (RRID:SCR_027718) Copy   

•   Source: SciCrunch Registry

https://github.com/atakanekiz/CIPR-Package

Software R package for annotating cell clusters in scRNAseq data.

Proper citation: CIPR-Package (RRID:SCR_027697) 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