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https://benjjneb.github.io/dada2/
Open source software R package for modeling and correcting Illumina sequenced amplicon errors. Fast and accurate sample inference from amplicon data with single nucleotide resolution.
Proper citation: DADA2 (RRID:SCR_023519) Copy
https://github.com/cliu32/athlates
Software package for determining HLA genotypes for individuals from Illumina exome sequencing data. Program applies assembly, allele identification and allelic pair inference to short read sequences, and applies it to data from Illumina platforms.
Proper citation: ATHLATES (RRID:SCR_023689) Copy
An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples.
Proper citation: MG-RAST (RRID:SCR_004814) Copy
Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in.
Proper citation: CRCView (RRID:SCR_007092) 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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