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https://www.bioconductor.org/packages/release/bioc/html/imcRtools.html

Software R package that supports the handling and processing of IMC multiplex imaging data. Used for handling and analysing imaging mass cytometry data.

Proper citation: imcRtools (RRID:SCR_027613) Copy   

•   Source: SciCrunch Registry

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

Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods.

Proper citation: sandwich (RRID:SCR_027691) Copy   

•   Source: SciCrunch Registry

https://icahn.mssm.edu/research/human-immune-monitoring-center

Core provides team of experts in the characterization of immune profiles and treatment responses across a diverse range of diseases, such as cancer, autoimmunity, allergy, and neuro-immune disorders. Offers equipment in the field for research at Genomic, cellular and proteomic analysis. Develops assays to balance innovation with protocols and operating procedures to ensure data quality and reproducibility.

Proper citation: Icahn School of Medicine at Mount Sinai Human Immune Monitoring Center Core Facility (RRID:SCR_027571) Copy   

•   Source: SciCrunch Registry

https://github.com/ncc-gap/GCATWorkflow

Software cancer genome and RNA sequencing data analysis pipeline that detects genomic variants and transcriptomic changes.

Proper citation: GCAT Workflow (RRID:SCR_027692) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/csbayrak/ips

Software with approach that leverages machine learning and network biology to predict brain gene expression from blood-derived features.

Proper citation: Integrative Prediction Strategy (RRID:SCR_027608) Copy   

•   Source: SciCrunch Registry

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

Software R package for analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach.

Proper citation: ltm:Latent Trait Models under IRT (RRID:SCR_027664) Copy   

•   Source: SciCrunch Registry

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

Software R package for latent variable analysis. Used to estimate variety of multivariate statistical models. Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.

Proper citation: lavaan (RRID:SCR_027663) Copy   

•   Source: SciCrunch Registry

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/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://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://github.com/BioDepot/SpatialProteomics

Software graphical and containerized spatial proteomics workflow. End-to-end containerized spatial proteomics analysis workflow with QuPath integration. Consists of cell segmentation, batch correction, unsupervised clustering, validation of clusters on the image, and cell type clustering results visualization.

Proper citation: SpatialProteomics (RRID:SCR_027835) Copy   

•   Source: SciCrunch Registry