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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://cibersort.stanford.edu/
Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.
Proper citation: CIBERSORT (RRID:SCR_016955) Copy
Software Python package to automate building of ML pipelines by combining flexible expression tree representation of pipelines with stochastic search algorithms such as genetic programming.
Proper citation: Tree-Based Pipeline Optimization Tool (RRID:SCR_017531) Copy
https://psbweb05.psb.ugent.be/conet/microbialnetworks/spieceasi.php
Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets.
Proper citation: Sparse Inverse Covariance Estimation for Ecological Association Inference (RRID:SCR_022646) Copy
Central data repository that supplies organisms and reagents to the broad community of microbiology and infectious diseases researchers.
Proper citation: BEI Resource Repository (RRID:SCR_013698) Copy
http://coreimmunology.ucsf.edu/flow-cytometry
Flow cytometry facility offering training and services including:Access to two, 17-color BD LSR II analytical instruments with High Throughput Sampler (HTS) module,Configurations:LSRII 1,LSRII 2;Help with Flow Cytometry Panel Design;Fluorofinder (access our cytometers under CFAR Immunology Core);BD Panel designer;SFGH LSRII Flow Core Protocols;LSRII Startup and Shutdown;How to run the CST calibration assay;Access to a 17-color BD FACSAria II for fluorescence-activated cell sorting (FACS);4-way tube sorting;96 well plate sorting;Index sorting;SFGH ARIA Flow Core Protocols and configuration;ARIA Startup;Determining Drop Delay;Side Stream Set Up;Clog Procedure;ARIA Shutdown Protocol;ARIA Configuration;DNA analysis with standard dyes;Analysis of CFP, GFP, YFP, mRFP, mTomato, and mCherry gene expression proteins;Calcium flux measurements using Indo-1;Training of users on the operation of instruments and experimental design through the CIL Flow Cytometry Course;Maintaining and Upgrading Instruments;Research Support Services (study design, assay selection, grant and paper writing support).
Proper citation: University of California at San Francisco Division of Experimental Medicine Flow Core Facility (RRID:SCR_017903) Copy
https://github.com/mwang87/MassQueryLanguage
Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data.
Proper citation: MassQL (RRID:SCR_025106) Copy
https://github.com/sxf296/drug_targeting
Software tool to detect phenotypically relevant drug targets through unique transcriptomic enrichment that emphasizes biological directionality of drug-derived gene sets. Exploratory tool to screen for possible drug targeting molecules.
Proper citation: drug perturbation Gene Set Enrichment Analysis (RRID:SCR_025351) Copy
https://github.com/immunogenomics/masc
Software tool for testing whether specified covariate influences membership of single cells in any of multiple cellular subsets while accounting for technical confounds and biological variation.
Proper citation: Mixed effects association testing for single cells (RRID:SCR_025632) Copy
https://github.com/dviraran/xCell
Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis.
Proper citation: xCell (RRID:SCR_026446) Copy
https://github.com/GreenleafLab/chromVAR
Software R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. Enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility. Used for analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data.
Proper citation: chromvar (RRID:SCR_026570) Copy
https://github.com/RGLab/CytoML
Software R package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R.
Proper citation: CytoML (RRID:SCR_027485) Copy
https://github.com/VincentGardeux/demuxlet?tab=readme-ov-file
Software tool that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). Genetic multiplexing of barcoded single cell RNA-seq.
Proper citation: demuxlet (RRID:SCR_027855) Copy
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